第一次merge

Add CI job for Ubuntu 20.04 aarch64

.github/workflows/ci.yaml

@@ -0,0 +1,46 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout bwa
+      uses: actions/checkout@v3
+
+    - name: Compile with ${{ matrix.compiler }}
+      run:  make CC=${{ matrix.compiler }}
+
+  build-aarch64:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout bwa
+      uses: actions/checkout@v3
+
+    - name: Compile with ${{ matrix.compiler }}
+      uses: uraimo/run-on-arch-action@v2
+      with:
+        arch: aarch64
+        distro: ubuntu20.04
+        githubToken: ${{ github.token }}
+        dockerRunArgs: |
+          --volume "${PWD}:/bwa"
+        install: |
+          apt-get update -q -y
+          apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev
+        run: |
+          cd /bwa
+          make CC=${{ matrix.compiler }}

.gitignore

@@ -1,3 +1,10 @@
+*.[oa]
+bwa
+test
+test64
+.*.swp
+Makefile.bak
+bwamem-lite
 # ---> C
 # Prerequisites
 *.d
@@ -51,4 +58,3 @@ modules.order
 Module.symvers
 Mkfile.old
 dkms.conf
-

.vscode/launch.json

@@ -0,0 +1,41 @@
+{
+    // 使用 IntelliSense 了解相关属性。 
+    // 悬停以查看现有属性的描述。
+    // 欲了解更多信息，请访问: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "bwa-mem",
+            "preLaunchTask": "Build",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceRoot}/bwa",
+            "args": [
+                "mem",
+                "-t",
+                "1",
+                "-M",
+                "-R",
+                "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
+                "/home/zzh/data/reference/human_g1k_v37_decoy.fasta",
+                "/home/zzh/data/fastq/n_s1.fq",
+                "/home/zzh/data/fastq/n_s2.fq",
+                "-o",
+                "/dev/null"
+            ],
+            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
+        },
+        {
+            "name": "index",
+            "preLaunchTask": "Build",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceRoot}/bwa",
+            "args": [
+                "index",
+                "/mnt/d/data/reference/human_g1k_v37_decoy.fasta"
+            ],
+            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,13 @@
+{
+    "files.associations": {
+        "bwt.h": "c",
+        "bwa.h": "c",
+        "malloc_wrap.h": "c",
+        "bntseq.h": "c",
+        "utils.h": "c",
+        "rle.h": "c",
+        "rope.h": "c",
+        "random": "c",
+        "kseq.h": "c"
+    }
+}

.vscode/tasks.json

@@ -0,0 +1,17 @@
+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "Build",
+            "type": "shell",
+            "command": "make clean; make -j 16",
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            }
+        }
+    ]
+}

COPYING

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
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+  A patent license is "discriminatory" if it does not include within
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+
+  Nothing in this License shall be construed as excluding or limiting
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+
+  12. No Surrender of Others' Freedom.
+
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+
+  13. Use with the GNU Affero General Public License.
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+  14. Revised Versions of this License.
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+
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+  17. Interpretation of Sections 15 and 16.
+
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+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

Makefile

@@ -0,0 +1,89 @@
+CC=			gcc
+#CC=			clang --analyze
+# CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS=		-g -Wall -Wno-unused-function #-O2
+WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+AR=			ar
+DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
+			QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
+AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+			bwape.o kopen.o pemerge.o maxk.o \
+			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
+			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
+PROG=		bwa
+INCLUDES=	
+LIBS=		-lm -lz -lpthread
+SUBDIRS=	.
+
+ifeq ($(shell uname -s),Linux)
+	LIBS += -lrt
+endif
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $(CPPFLAGS) $< -o $@
+
+all:$(PROG)
+
+bwa:libbwa.a $(AOBJS) main.o
+		$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+bwamem-lite:libbwa.a example.o
+		$(CC) $(CFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+
+libbwa.a:$(LOBJS)
+		$(AR) -csru $@ $(LOBJS)
+
+clean:
+		rm -f gmon.out *.o a.out $(PROG) *~ *.a
+
+depend:
+	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) $(CPPFLAGS) -- *.c )
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
+QSufSort.o: QSufSort.h
+bamlite.o: bamlite.h malloc_wrap.h
+bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h
+bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kvec.h
+bwa.o: kseq.h
+bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
+bwamem.o: ksort.h utils.h kbtree.h
+bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h
+bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
+bwamem_pair.o: utils.h ksw.h
+bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
+bwape.o: ksw.h khash.h
+bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
+bwase.o: bwa.h ksw.h
+bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
+bwashm.o: bwa.h bntseq.h bwt.h
+bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
+bwt_gen.o: QSufSort.h malloc_wrap.h
+bwt_lite.o: bwt_lite.h malloc_wrap.h
+bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
+bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
+bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h
+bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
+bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
+bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
+bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
+bwtsw2_core.o: khash.h ksort.h
+bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
+bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
+bwtsw2_pair.o: malloc_wrap.h ksw.h
+example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
+fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
+is.o: malloc_wrap.h
+kopen.o: malloc_wrap.h
+kstring.o: kstring.h malloc_wrap.h
+ksw.o: ksw.h neon_sse.h scalar_sse.h malloc_wrap.h
+main.o: kstring.h malloc_wrap.h utils.h
+malloc_wrap.o: malloc_wrap.h
+maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h
+pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
+rle.o: rle.h
+rope.o: rle.h rope.h
+utils.o: utils.h ksort.h malloc_wrap.h kseq.h

QSufSort.c

@@ -0,0 +1,402 @@
+/* QSufSort.c
+
+   Original source from qsufsort.c
+
+   Copyright 1999, N. Jesper Larsson, all rights reserved.
+
+   This file contains an implementation of the algorithm presented in "Faster
+   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
+   Sadakane (sada@is.s.u-tokyo.ac.jp).
+
+   This software may be used freely for any purpose. However, when distributed,
+   the original source must be clearly stated, and, when the source code is
+   distributed, the copyright notice must be retained and any alterations in
+   the code must be clearly marked. No warranty is given regarding the quality
+   of this software.
+
+   Modified by Wong Chi-Kwong, 2004
+
+   Changes summary:	- Used long variable and function names
+					- Removed global variables
+					- Replace pointer references with array references
+					- Used insertion sort in place of selection sort and increased insertion sort threshold
+					- Reconstructing suffix array from inverse becomes an option
+					- Add handling where end-of-text symbol is not necessary < all characters
+					- Removed codes for supporting alphabet size > number of characters
+  
+  No warrenty is given regarding the quality of the modifications.
+
+*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "QSufSort.h"
+
+#define min(value1, value2)						( ((value1) < (value2)) ? (value1) : (value2) )
+#define med3(a, b, c)							( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
+#define swap(a, b, t);							t = a; a = b; b = t;
+
+// Static functions
+static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+							  const qsint_t highestPos, const qsint_t numSortedChar);
+static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+							   const qsint_t highestPos, const qsint_t numSortedChar);
+static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+									const qsint_t highestPos, const qsint_t numSortedChar);
+static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize);
+static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
+							 const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated);
+
+/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
+   n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
+   contents of x[n] is disregarded, the n-th symbol being regarded as
+   end-of-string smaller than all other symbols.*/
+void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
+						const qsint_t smallestInputSymbol, const int skipTransform)
+{
+	qsint_t i, j;
+	qsint_t s, negatedSortedGroupLength;
+	qsint_t numSymbolAggregated;
+	qsint_t numSortedPos = 1;
+	qsint_t newAlphabetSize;
+   
+	if (!skipTransform) {
+		/* bucketing possible*/
+		newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol, 
+											numChar, &numSymbolAggregated);
+		QSufSortBucketSort(V, I, numChar, newAlphabetSize);
+		I[0] = -1;
+		V[numChar] = 0;
+		numSortedPos = numSymbolAggregated;
+	}
+
+	while ((qsint_t)(I[0]) >= -(qsint_t)numChar) {
+		i = 0;
+		negatedSortedGroupLength = 0;
+		do {
+			s = I[i];
+			if (s < 0) {
+				i -= s;						/* skip over sorted group.*/
+				negatedSortedGroupLength += s;
+			} else {
+				if (negatedSortedGroupLength) {
+					I[i+negatedSortedGroupLength] = negatedSortedGroupLength;	/* combine preceding sorted groups */
+					negatedSortedGroupLength = 0;
+				}
+				j = V[s] + 1;
+				QSufSortSortSplit(V, I, i, j - 1, numSortedPos);
+				i = j;
+			}
+		} while (i <= numChar);
+		if (negatedSortedGroupLength) {
+			/* array ends with a sorted group.*/
+			I[i+negatedSortedGroupLength] = negatedSortedGroupLength;	/* combine sorted groups at end of I.*/
+		}
+		numSortedPos *= 2;	/* double sorted-depth.*/
+	}
+}
+
+void QSufSortGenerateSaFromInverse(const qsint_t* V, qsint_t* __restrict I, const qsint_t numChar)
+{
+	qsint_t i;
+	for (i=0; i<=numChar; i++)
+		I[V[i]] = i + 1;
+}
+
+/* Sorting routine called for each unsorted group. Sorts the array of integers
+   (suffix numbers) of length n starting at p. The algorithm is a ternary-split
+   quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
+   Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
+   function is based on Program 7.*/
+static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+							  const qsint_t highestPos, const qsint_t numSortedChar) {
+
+	qsint_t a, b, c, d;
+	qsint_t l, m;
+	qsint_t f, v, s, t;
+	qsint_t tmp;
+	qsint_t numItem;
+
+	numItem = highestPos - lowestPos + 1;
+
+	if (numItem <= INSERT_SORT_NUM_ITEM) {
+		QSufSortInsertSortSplit(V, I, lowestPos, highestPos, numSortedChar);
+		return;
+	}
+
+	v = QSufSortChoosePivot(V, I, lowestPos, highestPos, numSortedChar);
+
+	a = b = lowestPos;
+	c = d = highestPos;
+
+	while (1) {
+		while (c >= b && (f = KEY(V, I, b, numSortedChar)) <= v) {
+			if (f == v) {
+				swap(I[a], I[b], tmp);
+				a++;
+			}
+			b++;
+		}
+		while (c >= b && (f = KEY(V, I, c, numSortedChar)) >= v) {
+			if (f == v) {
+				swap(I[c], I[d], tmp);
+				d--;
+			}
+			c--;
+		}
+		if (b > c)
+			break;
+		swap(I[b], I[c], tmp);
+		b++;
+		c--;
+	}
+
+	s = a - lowestPos;
+	t = b - a;
+	s = min(s, t);
+	for (l = lowestPos, m = b - s; m < b; l++, m++) {
+		swap(I[l], I[m], tmp);
+	}
+
+	s = d - c;
+	t = highestPos - d;
+	s = min(s, t);
+	for (l = b, m = highestPos - s + 1; m <= highestPos; l++, m++) {
+		swap(I[l], I[m], tmp);
+	}
+
+	s = b - a;
+	t = d - c;
+	if (s > 0)
+		QSufSortSortSplit(V, I, lowestPos, lowestPos + s - 1, numSortedChar);
+
+	// Update group number for equal portion
+	a = lowestPos + s;
+	b = highestPos - t;
+	if (a == b) {
+		// Sorted group
+		V[I[a]] = a;
+		I[a] = -1;
+	} else {
+		// Unsorted group
+		for (c=a; c<=b; c++)
+			V[I[c]] = b;
+	}
+
+	if (t > 0)
+		QSufSortSortSplit(V, I, highestPos - t + 1, highestPos, numSortedChar);
+
+}
+
+/* Algorithm by Bentley & McIlroy.*/
+static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+							   const qsint_t highestPos, const qsint_t numSortedChar) {
+
+	qsint_t m;
+	qsint_t keyl, keym, keyn;
+	qsint_t key1, key2, key3;
+	qsint_t s;
+	qsint_t numItem;
+
+	numItem = highestPos - lowestPos + 1;
+
+	m = lowestPos + numItem / 2;
+
+	s = numItem / 8;
+	key1 = KEY(V, I, lowestPos, numSortedChar);
+	key2 = KEY(V, I, lowestPos+s, numSortedChar);
+	key3 = KEY(V, I, lowestPos+2*s, numSortedChar);
+	keyl = med3(key1, key2, key3);
+	key1 = KEY(V, I, m-s, numSortedChar);
+	key2 = KEY(V, I, m, numSortedChar);
+	key3 = KEY(V, I, m+s, numSortedChar);
+	keym = med3(key1, key2, key3);
+	key1 = KEY(V, I, highestPos-2*s, numSortedChar);
+	key2 = KEY(V, I, highestPos-s, numSortedChar);
+	key3 = KEY(V, I, highestPos, numSortedChar);
+	keyn = med3(key1, key2, key3);
+
+	return med3(keyl, keym, keyn);
+
+
+}
+
+/* Quadratic sorting method to use for small subarrays. */
+static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
+									const qsint_t highestPos, const qsint_t numSortedChar)
+{
+	qsint_t i, j;
+	qsint_t tmpKey, tmpPos;
+	qsint_t numItem;
+	qsint_t key[INSERT_SORT_NUM_ITEM], pos[INSERT_SORT_NUM_ITEM];
+	qsint_t negativeSortedLength;
+	qsint_t groupNum;
+
+	numItem = highestPos - lowestPos + 1;
+
+	for (i=0; i<numItem; i++) {
+		pos[i] = I[lowestPos + i];
+		key[i] = V[pos[i] + numSortedChar];
+	}
+
+	for (i=1; i<numItem; i++) {
+		tmpKey = key[i];
+		tmpPos = pos[i];
+		for (j=i; j>0 && key[j-1] > tmpKey; j--) {
+			key[j] = key[j-1];
+			pos[j] = pos[j-1];
+		}
+		key[j] = tmpKey;
+		pos[j] = tmpPos;
+	}
+
+	negativeSortedLength = -1;
+
+	i = numItem - 1;
+	groupNum = highestPos;
+	while (i > 0) {
+		I[i+lowestPos] = pos[i];
+		V[I[i+lowestPos]] = groupNum;
+		if (key[i-1] == key[i]) {
+			negativeSortedLength = 0;
+		} else {
+			if (negativeSortedLength < 0)
+				I[i+lowestPos] = negativeSortedLength;
+			groupNum = i + lowestPos - 1;
+			negativeSortedLength--;
+		}
+		i--;
+	}
+
+	I[lowestPos] = pos[0];
+	V[I[lowestPos]] = groupNum;
+	if (negativeSortedLength < 0)
+		I[lowestPos] = negativeSortedLength;
+}
+
+/* Bucketsort for first iteration.
+
+   Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
+   at least once. x[n] is 0. (This is the corresponding output of transform.) k
+   must be at most n+1. p is array of size n+1 whose contents are disregarded.
+
+   Output: x is V and p is I after the initial sorting stage of the refined
+   suffix sorting algorithm.*/
+      
+static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize)
+{
+	qsint_t i, c;
+	qsint_t d;
+	qsint_t groupNum;
+	qsint_t currentIndex;
+
+	// mark linked list empty
+	for (i=0; i<alphabetSize; i++)
+		I[i] = -1;
+
+	// insert to linked list
+	for (i=0; i<=numChar; i++) {
+		c = V[i];
+		V[i] = (qsint_t)(I[c]);
+		I[c] = i;
+	}
+
+	currentIndex = numChar;
+	for (i=alphabetSize; i>0; i--) {
+		c = I[i-1];
+		d = (qsint_t)(V[c]);
+		groupNum = currentIndex;
+		V[c] = groupNum;
+		if (d >= 0) {
+			I[currentIndex] = c;
+			while (d >= 0) {
+				c = d;
+				d = V[c];
+				V[c] = groupNum;
+				currentIndex--;
+				I[currentIndex] = c;
+			}
+		} else {
+			// sorted group
+			I[currentIndex] = -1;
+		}
+		currentIndex--;
+	}
+}
+
+/* Transforms the alphabet of x by attempting to aggregate several symbols into
+   one, while preserving the suffix order of x. The alphabet may also be
+   compacted, so that x on output comprises all integers of the new alphabet
+   with no skipped numbers.
+
+   Input: x is an array of size n+1 whose first n elements are positive
+   integers in the range l...k-1. p is array of size n+1, used for temporary
+   storage. q controls aggregation and compaction by defining the maximum intue
+   for any symbol during transformation: q must be at least k-l; if q<=n,
+   compaction is guaranteed; if k-l>n, compaction is never done; if q is
+   INT_MAX, the maximum number of symbols are aggregated into one.
+   
+   Output: Returns an integer j in the range 1...q representing the size of the
+   new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
+   set to the number of old symbols grouped into one. Only x[n] is 0.*/
+static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
+							 const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated)
+{
+	qsint_t c, i, j;
+	qsint_t a;	// numSymbolAggregated
+	qsint_t mask;
+	qsint_t minSymbolInChunk = 0, maxSymbolInChunk = 0;
+	qsint_t newAlphabetSize;
+	qsint_t maxNumInputSymbol, maxNumBit, maxSymbol;
+
+	maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;
+
+	for (maxNumBit = 0, i = maxNumInputSymbol; i; i >>= 1) ++maxNumBit;
+	maxSymbol = QSINT_MAX >> maxNumBit;
+
+	c = maxNumInputSymbol;
+	for (a = 0; a < numChar && maxSymbolInChunk <= maxSymbol && c <= maxNewAlphabetSize; a++) {
+		minSymbolInChunk = (minSymbolInChunk << maxNumBit) | (V[a] - smallestInputSymbol + 1);
+		maxSymbolInChunk = c;
+		c = (maxSymbolInChunk << maxNumBit) | maxNumInputSymbol;
+	}
+
+	mask = (1 << (a-1) * maxNumBit) - 1;	/* mask masks off top old symbol from chunk.*/
+	V[numChar] = smallestInputSymbol - 1;	/* emulate zero terminator.*/
+
+	/* bucketing possible, compact alphabet.*/
+	for (i=0; i<=maxSymbolInChunk; i++)
+		I[i] = 0;	/* zero transformation table.*/
+	c = minSymbolInChunk;
+	for (i=a; i<=numChar; i++) {
+		I[c] = 1;			/* mark used chunk symbol.*/
+		c = ((c & mask) << maxNumBit) | (V[i] - smallestInputSymbol + 1);	/* shift in next old symbol in chunk.*/
+	}
+	for (i=1; i<a; i++) {	/* handle last r-1 positions.*/
+		I[c] = 1;			/* mark used chunk symbol.*/
+		c = (c & mask) << maxNumBit;	/* shift in next old symbol in chunk.*/
+	}
+	newAlphabetSize = 1;
+	for (i=0; i<=maxSymbolInChunk; i++) {
+		if (I[i]) {
+			I[i] = newAlphabetSize;
+			newAlphabetSize++;
+		}
+	}
+	c = minSymbolInChunk;
+	for (i=0, j=a; j<=numChar; i++, j++) {
+		V[i] = I[c];						/* transform to new alphabet.*/
+		c = ((c & mask) << maxNumBit) | (V[j] - smallestInputSymbol + 1);	/* shift in next old symbol in chunk.*/
+	}
+	for (; i<numChar; i++) {	/* handle last a-1 positions.*/
+		V[i] = I[c];			/* transform to new alphabet.*/
+		c = (c & mask) << maxNumBit;	/* shift right-end zero in chunk.*/
+	}
+
+	V[numChar] = 0;		/* end-of-string symbol is zero.*/
+
+    *numSymbolAggregated = a;
+	return newAlphabetSize;
+}

QSufSort.h

@@ -0,0 +1,45 @@
+/* QSufSort.h
+
+   Header file for QSufSort.c
+
+   This file contains an implementation of the algorithm presented in "Faster
+   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
+   Sadakane (sada@is.s.u-tokyo.ac.jp).
+
+   This software may be used freely for any purpose. However, when distributed,
+   the original source must be clearly stated, and, when the source code is
+   distributed, the copyright notice must be retained and any alterations in
+   the code must be clearly marked. No warranty is given regarding the quality
+   of this software.
+
+   Modified by Wong Chi-Kwong, 2004
+
+   Changes summary:	- Used long variable and function names
+					- Removed global variables
+					- Replace pointer references with array references
+					- Used insertion sort in place of selection sort and increased insertion sort threshold
+					- Reconstructing suffix array from inverse becomes an option
+					- Add handling where end-of-text symbol is not necessary < all characters
+					- Removed codes for supporting alphabet size > number of characters
+  
+  No warrenty is given regarding the quality of the modifications.
+
+*/
+
+#ifndef __QSUFSORT_H__
+#define __QSUFSORT_H__
+
+#include <stdint.h>
+
+#define KEY(V, I, p, h)					( V[ I[p] + h ] )
+#define INSERT_SORT_NUM_ITEM	16
+
+typedef int64_t qsint_t;
+#define QSINT_MAX INT64_MAX
+
+void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
+						const qsint_t smallestInputSymbol, const int skipTransform);
+void QSufSortGenerateSaFromInverse(const qsint_t *V, qsint_t* __restrict I, const qsint_t numChar);
+
+
+#endif

README-alt.md

@@ -0,0 +1,178 @@
+## For the Impatient
+
+```sh
+# Download bwakit (or from <http://sourceforge.net/projects/bio-bwa/files/bwakit/> manually)
+wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2/download \
+  | gzip -dc | tar xf -
+# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
+bwa.kit/run-gen-ref hs38DH   # download GRCh38 and write hs38DH.fa
+bwa.kit/bwa index hs38DH.fa  # create BWA index
+# mapping
+bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh  # skip "|sh" to show command lines
+```
+
+This generates `out.aln.bam` as the final alignment, `out.hla.top` for best HLA
+genotypes on each gene and `out.hla.all` for other possible HLA genotypes.
+Please check out [bwa/bwakit/README.md][kithelp] for details.
+
+## Background
+
+GRCh38 consists of several components: chromosomal assembly, unlocalized contigs
+(chromosome known but location unknown), unplaced contigs (chromosome unknown)
+and ALT contigs (long clustered variations). The combination of the first three
+components is called the *primary assembly*. It is recommended to use the
+complete primary assembly for all analyses. Using ALT contigs in read mapping is
+tricky.
+
+GRCh38 ALT contigs are totaled 109Mb in length, spanning 60Mbp of the primary
+assembly. However, sequences that are highly diverged from the primary assembly
+only contribute a few million bp. Most subsequences of ALT contigs are nearly
+identical to the primary assembly. If we align sequence reads to GRCh38+ALT
+blindly, we will get many additional reads with zero mapping quality and miss
+variants on them. It is crucial to make mappers aware of ALTs.
+
+BWA-MEM is ALT-aware. It essentially computes mapping quality across the
+non-redundant content of the primary assembly plus the ALT contigs and is free
+of the problem above.
+
+## Methods
+
+### Sequence alignment
+
+As of now, ALT mapping is done in two separate steps: BWA-MEM mapping and
+postprocessing. The `bwa.kit/run-bwamem` script performs the two steps when ALT
+contigs are present. The following picture shows an example about how BWA-MEM
+infers mapping quality and reports alignment after step 2:
+
+![](http://lh3lh3.users.sourceforge.net/images/alt-demo.png)
+
+#### Step 1: BWA-MEM mapping
+
+At this step, BWA-MEM reads the ALT contig names from "*idxbase*.alt", ignoring
+the ALT-to-ref alignment, and labels a potential hit as *ALT* or *non-ALT*,
+depending on whether the hit lands on an ALT contig or not. BWA-MEM then reports
+alignments and assigns mapQ following these two rules:
+
+1. The mapQ of a non-ALT hit is computed across non-ALT hits only. The mapQ of
+   an ALT hit is computed across all hits.
+
+2. If there are no non-ALT hits, the best ALT hit is outputted as the primary
+   alignment. If there are both ALT and non-ALT hits, non-ALT hits will be
+   primary and ALT hits be supplementary (SAM flag 0x800).
+
+In theory, non-ALT alignments from step 1 should be identical to alignments
+against the reference genome with ALT contigs. In practice, the two types of
+alignments may differ in rare cases due to seeding heuristics. When an ALT hit
+is significantly better than non-ALT hits, BWA-MEM may miss seeds on the
+non-ALT hits.
+
+If we don't care about ALT hits, we may skip postprocessing (step 2).
+Nonetheless, postprocessing is recommended as it improves mapQ and gives more
+information about ALT hits.
+
+#### Step 2: Postprocessing
+
+Postprocessing is done with a separate script `bwa-postalt.js`. It reads all
+potential hits reported in the XA tag, lifts ALT hits to the chromosomal
+positions using the ALT-to-ref alignment, groups them based on overlaps between
+their lifted positions, and then re-estimates mapQ across the best scoring hit
+in each group. Being aware of the ALT-to-ref alignment, this script can greatly
+improve mapQ of ALT hits and occasionally improve mapQ of non-ALT hits. It also
+writes each hit overlapping the reported hit into a separate SAM line. This
+enables variant calling on each ALT contig independent of others.
+
+### On the completeness of GRCh38+ALT
+
+While GRCh38 is much more complete than GRCh37, it is still missing some true
+human sequences. To make sure every piece of sequence in the reference assembly
+is correct, the [Genome Reference Consortium][grc] (GRC) require each ALT contig
+to have enough support from multiple sources before considering to add it to the
+reference assembly. This careful and sophisticated procedure has left out some
+sequences, one of which is [this example][novel], a 10kb contig assembled from
+CHM1 short reads and present also in NA12878. You can try [BLAT][blat] or
+[BLAST][blast] to see where it maps.
+
+For a more complete reference genome, we compiled a new set of decoy sequences
+from GenBank clones and the de novo assembly of 254 public [SGDP][sgdp] samples.
+The sequences are included in `hs38DH-extra.fa` from the [BWA binary
+package][res].
+
+In addition to decoy, we also put multiple alleles of HLA genes in
+`hs38DH-extra.fa`. These genomic sequences were acquired from [IMGT/HLA][hladb],
+version 3.18.0 and are used to collect reads sequenced from these genes.
+
+### HLA typing
+
+HLA genes are known to be associated with many autoimmune diseases, infectious
+diseases and drug responses. They are among the most important genes but are
+rarely studied by WGS projects due to the high sequence divergence between
+HLA genes and the reference genome in these regions.
+
+By including the HLA gene regions in the reference assembly as ALT contigs, we
+are able to effectively identify reads coming from these genes. We also provide
+a pipeline, which is included in the [BWA binary package][res], to type the
+several classic HLA genes. The pipeline is conceptually simple. It de novo
+assembles sequence reads mapped to each gene, aligns exon sequences of each
+allele to the assembled contigs and then finds the pairs of alleles that best
+explain the contigs. In practice, however, the completeness of IMGT/HLA and
+copy-number changes related to these genes are not so straightforward to
+resolve. HLA typing may not always be successful. Users may also consider to use
+other programs for typing such as [Warren et al (2012)][hla4], [Liu et al
+(2013)][hla2], [Bai et al (2014)][hla3] and [Dilthey et al (2014)][hla1], though
+most of them are distributed under restrictive licenses.
+
+## Preliminary Evaluation
+
+To check whether GRCh38 is better than GRCh37, we mapped the CHM1 and NA12878
+unitigs to GRCh37 primary (hs37), GRCh38 primary (hs38) and GRCh38+ALT+decoy
+(hs38DH), and called small variants from the alignment. CHM1 is haploid.
+Ideally, heterozygous calls are false positives (FP). NA12878 is diploid. The
+true positive (TP) heterozygous calls from NA12878 are approximately equal
+to the difference between NA12878 and CHM1 heterozygous calls. A better assembly
+should yield higher TP and lower FP. The following table shows the numbers for
+these assemblies:
+
+|Assembly|hs37   |hs38   |hs38DH|CHM1_1.1|  huref|
+|:------:|------:|------:|------:|------:|------:|
+|FP      | 255706| 168068| 142516|307172 | 575634|
+|TP      |2142260|2163113|2150844|2167235|2137053|
+
+With this measurement, hs38 is clearly better than hs37. Genome hs38DH reduces
+FP by ~25k but also reduces TP by ~12k. We manually inspected variants called
+from hs38 only and found the majority of them are associated with excessive read
+depth, clustered variants or weak alignment. We believe most hs38-only calls are
+problematic. In addition, if we compare two NA12878 replicates from HiSeq X10
+with nearly identical library construction, the difference is ~140k, an order
+of magnitude higher than the difference between hs38 and hs38DH. ALT contigs,
+decoy and HLA genes in hs38DH improve variant calling and enable the analyses of
+ALT contigs and HLA typing at little cost.
+
+## Problems and Future Development
+
+There are some uncertainties about ALT mappings - we are not sure whether they
+help biological discovery and don't know the best way to analyze them. Without
+clear demand from downstream analyses, it is very difficult to design the
+optimal mapping strategy. The current BWA-MEM method is just a start. If it
+turns out to be useful in research, we will probably rewrite bwa-postalt.js in C
+for performance; if not, we may make changes. It is also possible that we might
+make breakthrough on the representation of multiple genomes, in which case, we
+can even get rid of ALT contigs for good.
+
+
+
+[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit
+[sb]: https://github.com/GregoryFaust/samblaster
+[grc]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
+[novel]: https://gist.github.com/lh3/9935148b71f04ba1a8cc
+[blat]: https://genome.ucsc.edu/cgi-bin/hgBlat
+[blast]: http://blast.st-va.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
+[sgdp]: http://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project/
+[hladb]: http://www.ebi.ac.uk/ipd/imgt/hla/
+[grcdef]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml
+[hla1]: http://biorxiv.org/content/early/2014/07/08/006973
+[hlalink]: http://www.hladiseaseassociations.com
+[hlatools]: https://www.biostars.org/p/93245/
+[hla2]: http://nar.oxfordjournals.org/content/41/14/e142.full.pdf+html
+[hla3]: http://www.biomedcentral.com/1471-2164/15/325
+[hla4]: http://genomemedicine.com/content/4/12/95
+[kithelp]: https://github.com/lh3/bwa/tree/master/bwakit

README.md

@@ -1,3 +1,189 @@
+[![Build Status](https://github.com/lh3/bwa/actions/workflows/ci.yaml/badge.svg)](https://github.com/lh3/bwa/actions)
+[![SourceForge Downloads](https://img.shields.io/sourceforge/dt/bio-bwa.svg?label=SF%20downloads)](https://sourceforge.net/projects/bio-bwa/files/?source=navbar)
+[![GitHub Downloads](https://img.shields.io/github/downloads/lh3/bwa/total.svg?style=flat&label=GitHub%20downloads)](https://github.com/lh3/bwa/releases)
+[![BioConda Install](https://img.shields.io/conda/dn/bioconda/bwa.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/bwa)
+
+**Note: [minimap2][minimap2] has replaced BWA-MEM for __PacBio and Nanopore__ read
+alignment.** It retains all major BWA-MEM features, but is ~50 times as fast,
+more versatile, more accurate and produces better base-level alignment.
+A beta version of [BWA-MEM2][bwa-mem2] has been released for short-read mapping.
+BWA-MEM2 is about twice as fast as BWA-MEM and outputs near identical alignments.
+
+[minimap2]: https://github.com/lh3/minimap2
+[bwa-mem2]: https://github.com/bwa-mem2/bwa-mem2
+
+## Getting started
+
+	git clone https://github.com/lh3/bwa.git
+	cd bwa; make
+	./bwa index ref.fa
+	./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
+	./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
+
+## Introduction
+
+BWA is a software package for mapping DNA sequences against a large reference
+genome, such as the human genome. It consists of three algorithms:
+BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
+sequence reads up to 100bp, while the rest two for longer sequences ranged from
+70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the
+support of long reads and chimeric alignment, but BWA-MEM, which is the latest,
+is generally recommended as it is faster and more accurate. BWA-MEM also has
+better performance than BWA-backtrack for 70-100bp Illumina reads.
+
+For all the algorithms, BWA first needs to construct the FM-index for the
+reference genome (the **index** command). Alignment algorithms are invoked with
+different sub-commands: **aln/samse/sampe** for BWA-backtrack,
+**bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.
+
+## Availability
+
+BWA is released under [GPLv3][1]. The latest source code is [freely
+available at github][2]. Released packages can [be downloaded][3] at
+SourceForge. After you acquire the source code, simply use `make` to compile
+and copy the single executable `bwa` to the destination you want. The only
+dependency required to build BWA is [zlib][14].
+
+Since 0.7.11, precompiled binary for x86\_64-linux is available in [bwakit][17].
+In addition to BWA, this self-consistent package also comes with bwa-associated
+and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs,
+adapter triming, duplicate marking, HLA typing and associated data files.
+
+## Seeking help
+
+The detailed usage is described in the man page available together with the
+source code. You can use `man ./bwa.1` to view the man page in a terminal. The
+[HTML version][4] of the man page can be found at the [BWA website][5]. If you
+have questions about BWA, you may [sign up the mailing list][6] and then send
+the questions to [bio-bwa-help@sourceforge.net][7]. You may also ask questions
+in forums such as [BioStar][8] and [SEQanswers][9].
+
+## Citing BWA
+
+* Li H. and Durbin R. (2009) Fast and accurate short read alignment with
+ Burrows-Wheeler transform. *Bioinformatics*, **25**, 1754-1760. [PMID:
+ [19451168][10]]. (if you use the BWA-backtrack algorithm)
+
+* Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
+ Burrows-Wheeler transform. *Bioinformatics*, **26**, 589-595. [PMID:
+ [20080505][11]]. (if you use the BWA-SW algorithm)
+
+* Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
+ with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
+ algorithm or the **fastmap** command, or want to cite the whole BWA package)
+
+Please note that the last reference is a preprint hosted at [arXiv.org][13]. I
+do not have plan to submit it to a peer-reviewed journal in the near future.
+
+## Frequently asked questions (FAQs)
+
+1. [What types of data does BWA work with?](#type)
+2. [Why does a read appear multiple times in the output SAM?](#multihit)
+3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb)
+4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0)
+5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
+6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg)
+7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt)
+
+#### <a name="type"></a>1. What types of data does BWA work with?
+
+BWA works with a variety types of DNA sequence data, though the optimal
+algorithm and setting may vary. The following list gives the recommended
+settings:
+
+* Illumina/454/IonTorrent single-end reads longer than ~70bp or assembly
+  contigs up to a few megabases mapped to a closely related reference genome:
+
+		bwa mem ref.fa reads.fq > aln.sam
+
+* Illumina single-end reads shorter than ~70bp:
+
+		bwa aln ref.fa reads.fq > reads.sai; bwa samse ref.fa reads.sai reads.fq > aln-se.sam
+
+* Illumina/454/IonTorrent paired-end reads longer than ~70bp:
+
+		bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
+
+* Illumina paired-end reads shorter than ~70bp:
+
+		bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai
+		bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam
+
+* PacBio subreads or Oxford Nanopore reads to a reference genome:
+
+		bwa mem -x pacbio ref.fa reads.fq > aln.sam
+		bwa mem -x ont2d ref.fa reads.fq > aln.sam
+
+BWA-MEM is recommended for query sequences longer than ~70bp for a variety of
+error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with
+errors given longer query sequences as the chance of missing all seeds is small.
+As is shown above, with non-default settings, BWA-MEM works with Oxford Nanopore
+reads with a sequencing error rate over 20%.
+
+#### <a name="multihit"></a>2. Why does a read appear multiple times in the output SAM?
+
+BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene
+fusion or a long deletion, a read bridging the break point may have two hits,
+occupying two lines in the SAM output. With the default setting of BWA-MEM, one
+and only one line is primary and is soft clipped; other lines are tagged with
+0x800 SAM flag (supplementary alignment) and are hard clipped.
+
+#### <a name="4gb"></a>3. Does BWA work on reference sequences longer than 4GB in total?
+
+Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over
+4GB. However, individual chromosome should not be longer than 2GB.
+
+#### <a name="pe0"></a>4. Why can one read in a pair have a high mapping quality but the other has zero?
+
+This is correct. Mapping quality is assigned for individual read, not for a read
+pair. It is possible that one read can be mapped unambiguously, but its mate
+falls in a tandem repeat and thus its accurate position cannot be determined.
+
+#### <a name="endref"></a>5. How can a BWA-backtrack alignment stand out of the end of a chromosome?
+
+Internally BWA concatenates all reference sequences into one long sequence. A
+read may be mapped to the junction of two adjacent reference sequences. In this
+case, BWA-backtrack will flag the read as unmapped (0x4), but you will see
+position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment
+as well. BWA-MEM does not have this problem.
+
+#### <a name="altctg"></a>6. Does BWA work with ALT contigs in the GRCh38 release?
+
+Yes, since 0.7.11, BWA-MEM officially supports mapping to GRCh38+ALT.
+BWA-backtrack and BWA-SW don't properly support ALT mapping as of now. Please
+see [README-alt.md][18] for details. Briefly, it is recommended to use
+[bwakit][17], the binary release of BWA, for generating the reference genome
+and for mapping.
+
+#### <a name="postalt"></a>7. Can I just run BWA-MEM against GRCh38+ALT without post-processing?
+
+If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM
+without post-processing. The alignments produced this way are very close to
+alignments against GRCh38 without ALT contigs. Nonetheless, applying
+post-processing helps to reduce false mappings caused by reads from the
+diverged part of ALT contigs and also enables HLA typing. It is recommended to
+run the post-processing script.
+
+
+
+[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
+[2]: https://github.com/lh3/bwa
+[3]: http://sourceforge.net/projects/bio-bwa/files/
+[4]: http://bio-bwa.sourceforge.net/bwa.shtml
+[5]: http://bio-bwa.sourceforge.net/
+[6]: https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
+[7]: mailto:bio-bwa-help@sourceforge.net
+[8]: http://biostars.org
+[9]: http://seqanswers.com/
+[10]: http://www.ncbi.nlm.nih.gov/pubmed/19451168
+[11]: http://www.ncbi.nlm.nih.gov/pubmed/20080505
+[12]: http://arxiv.org/abs/1303.3997
+[13]: http://arxiv.org/
+[14]: http://zlib.net/
+[15]: https://github.com/lh3/bwa/tree/mem
+[16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/
+[17]: http://sourceforge.net/projects/bio-bwa/files/bwakit/
+[18]: https://github.com/lh3/bwa/blob/master/README-alt.md
 # fast-bwa
 
-基于bwa，做一些优化，注释
+基于bwa，做一些优化，注释

bamlite.c

@@ -0,0 +1,210 @@
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include "bamlite.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+/*********************
+ * from bam_endian.c *
+ *********************/
+
+static inline int bam_is_big_endian()
+{
+	long one= 1;
+	return !(*((char *)(&one)));
+}
+static inline uint16_t bam_swap_endian_2(uint16_t v)
+{
+	return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
+}
+static inline void *bam_swap_endian_2p(void *x)
+{
+	*(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
+	return x;
+}
+static inline uint32_t bam_swap_endian_4(uint32_t v)
+{
+	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
+	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
+}
+static inline void *bam_swap_endian_4p(void *x)
+{
+	*(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
+	return x;
+}
+static inline uint64_t bam_swap_endian_8(uint64_t v)
+{
+	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
+	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
+	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
+}
+static inline void *bam_swap_endian_8p(void *x)
+{
+	*(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
+	return x;
+}
+
+/**************
+ * from bam.c *
+ **************/
+
+int bam_is_be;
+
+bam_header_t *bam_header_init()
+{
+	bam_is_be = bam_is_big_endian();
+	return (bam_header_t*)calloc(1, sizeof(bam_header_t));
+}
+
+void bam_header_destroy(bam_header_t *header)
+{
+	int32_t i;
+	if (header == 0) return;
+	if (header->target_name) {
+		for (i = 0; i < header->n_targets; ++i)
+			if (header->target_name[i]) free(header->target_name[i]);
+		if (header->target_len) free(header->target_len);
+		free(header->target_name);
+	}
+	if (header->text) free(header->text);
+	free(header);
+}
+
+bam_header_t *bam_header_read(bamFile fp)
+{
+	bam_header_t *header;
+	char buf[4];
+	int magic_len;
+	int32_t i = 1, name_len;
+	// read "BAM1"
+	magic_len = bam_read(fp, buf, 4);
+	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
+		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
+		return NULL;
+	}
+	header = bam_header_init();
+	// read plain text and the number of reference sequences
+	if (bam_read(fp, &header->l_text, 4) != 4) goto fail; 
+	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
+	header->text = (char*)calloc(header->l_text + 1, 1);
+	if (bam_read(fp, header->text, header->l_text) != header->l_text) goto fail;
+	if (bam_read(fp, &header->n_targets, 4) != 4) goto fail;
+	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
+	// read reference sequence names and lengths
+	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
+	header->target_len = (uint32_t*)calloc(header->n_targets, 4);
+	for (i = 0; i != header->n_targets; ++i) {
+		if (bam_read(fp, &name_len, 4) != 4) goto fail;
+		if (bam_is_be) bam_swap_endian_4p(&name_len);
+		header->target_name[i] = (char*)calloc(name_len, 1);
+		if (bam_read(fp, header->target_name[i], name_len) != name_len) {
+			goto fail;
+		}
+		if (bam_read(fp, &header->target_len[i], 4) != 4) goto fail;
+		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
+	}
+	return header;
+ fail:
+	bam_header_destroy(header);
+	return NULL;
+}
+
+static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
+{
+	uint8_t *s;
+	uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
+	s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
+	for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
+	while (s < data + data_len) {
+		uint8_t type;
+		s += 2; // skip key
+		type = toupper(*s); ++s; // skip type
+		if (type == 'C' || type == 'A') ++s;
+		else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
+		else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
+		else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
+		else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+	}
+}
+
+int bam_read1(bamFile fp, bam1_t *b)
+{
+	bam1_core_t *c = &b->core;
+	int32_t block_len, ret, i;
+	uint32_t x[8];
+
+	if ((ret = bam_read(fp, &block_len, 4)) != 4) {
+		if (ret == 0) return -1; // normal end-of-file
+		else return -2; // truncated
+	}
+	if (bam_read(fp, x, sizeof(bam1_core_t)) != sizeof(bam1_core_t)) return -3;
+	if (bam_is_be) {
+		bam_swap_endian_4p(&block_len);
+		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
+	}
+	c->tid = x[0]; c->pos = x[1];
+	c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
+	c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
+	c->l_qseq = x[4];
+	c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
+	b->data_len = block_len - sizeof(bam1_core_t);
+	if (b->m_data < b->data_len) {
+		b->m_data = b->data_len;
+		kroundup32(b->m_data);
+		b->data = (uint8_t*)realloc(b->data, b->m_data);
+	}
+	if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
+	b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
+	if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
+	return 4 + block_len;
+}
+
+
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+// Versions of gzopen, gzread and gzclose that print up error messages
+
+gzFile bamlite_gzopen(const char *fn, const char *mode) {
+	gzFile fp;
+	if (strcmp(fn, "-") == 0) {
+		fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+		if (!fp) {
+			fprintf(stderr, "Couldn't open %s : %s",
+					(strstr(mode, "r"))? "stdin" : "stdout",
+					strerror(errno));
+		}
+		return fp;
+	}
+	if ((fp = gzopen(fn, mode)) == 0) {
+		fprintf(stderr, "Couldn't open %s : %s\n", fn,
+				errno ? strerror(errno) : "Out of memory");
+	}
+	return fp;
+}
+
+int bamlite_gzread(gzFile file, void *ptr, unsigned int len) {
+	int ret = gzread(file, ptr, len);
+	
+	if (ret < 0) {
+		int errnum = 0;
+		const char *msg = gzerror(file, &errnum);
+		fprintf(stderr, "gzread error: %s\n",
+				Z_ERRNO == errnum ? strerror(errno) : msg);
+	}
+	return ret;
+}
+
+int bamlite_gzclose(gzFile file) {
+	int ret = gzclose(file);
+	if (Z_OK != ret) {
+		fprintf(stderr, "gzclose error: %s\n",
+						  Z_ERRNO == ret ? strerror(errno) : zError(ret));
+	}
+	
+	return ret;
+}
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */

bamlite.h

@@ -0,0 +1,114 @@
+#ifndef BAMLITE_H_
+#define BAMLITE_H_
+
+#include <stdint.h>
+#include <zlib.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define USE_VERBOSE_ZLIB_WRAPPERS
+
+typedef gzFile bamFile;
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+/* These print error messages on failure */
+#  define bam_open(fn, mode)      bamlite_gzopen(fn, mode)
+#  define bam_dopen(fd, mode)     gzdopen(fd, mode)
+#  define bam_close(fp)           bamlite_gzclose(fp)
+#  define bam_read(fp, buf, size) bamlite_gzread(fp, buf, size)
+#else
+#  define bam_open(fn, mode)      gzopen(fn, mode)
+#  define bam_dopen(fd, mode)     gzdopen(fd, mode)
+#  define bam_close(fp)           gzclose(fp)
+#  define bam_read(fp, buf, size) gzread(fp, buf, size)
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
+
+typedef struct {
+	int32_t n_targets;
+	char **target_name;
+	uint32_t *target_len;
+	size_t l_text, n_text;
+	char *text;
+} bam_header_t;
+
+#define BAM_FPAIRED        1
+#define BAM_FPROPER_PAIR   2
+#define BAM_FUNMAP         4
+#define BAM_FMUNMAP        8
+#define BAM_FREVERSE      16
+#define BAM_FMREVERSE     32
+#define BAM_FREAD1        64
+#define BAM_FREAD2       128
+#define BAM_FSECONDARY   256
+#define BAM_FQCFAIL      512
+#define BAM_FDUP        1024
+
+#define BAM_CIGAR_SHIFT 4
+#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)
+
+#define BAM_CMATCH      0
+#define BAM_CINS        1
+#define BAM_CDEL        2
+#define BAM_CREF_SKIP   3
+#define BAM_CSOFT_CLIP  4
+#define BAM_CHARD_CLIP  5
+#define BAM_CPAD        6
+
+typedef struct {
+	int32_t tid;
+	int32_t pos;
+	uint32_t bin:16, qual:8, l_qname:8;
+	uint32_t flag:16, n_cigar:16;
+	int32_t l_qseq;
+	int32_t mtid;
+	int32_t mpos;
+	int32_t isize;
+} bam1_core_t;
+
+typedef struct {
+	bam1_core_t core;
+	int l_aux, data_len, m_data;
+	uint8_t *data;
+} bam1_t;
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
+#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
+#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
+#define bam1_qname(b) ((char*)((b)->data))
+#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
+#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
+#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
+
+#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
+#define bam_destroy1(b) do {					\
+		if (b) { free((b)->data); free(b); }	\
+	} while (0)
+
+extern int bam_is_be;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bam_header_t *bam_header_init(void);
+	void bam_header_destroy(bam_header_t *header);
+	bam_header_t *bam_header_read(bamFile fp);
+	int bam_read1(bamFile fp, bam1_t *b);
+
+#ifdef USE_VERBOSE_ZLIB_WRAPPERS
+	gzFile bamlite_gzopen(const char *fn, const char *mode);
+	int bamlite_gzread(gzFile file, void *ptr, unsigned int len);
+	int bamlite_gzclose(gzFile file);
+#endif /* USE_VERBOSE_ZLIB_WRAPPERS */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bntseq.c

@@ -0,0 +1,451 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <unistd.h>
+#include <errno.h>
+#include "bntseq.h"
+#include "utils.h"
+
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(str, int)
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+unsigned char nst_nt4_table[256] = {
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 5 /*'-'*/, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
+};
+
+void bns_dump(const bntseq_t *bns, const char *prefix)
+{
+	char str[1024];
+	FILE *fp;
+	int i;
+	{ // dump .ann
+		strcpy(str, prefix); strcat(str, ".ann");
+		fp = xopen(str, "w");
+		err_fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
+		for (i = 0; i != bns->n_seqs; ++i) {
+			bntann1_t *p = bns->anns + i;
+			err_fprintf(fp, "%d %s", p->gi, p->name);
+			if (p->anno[0]) err_fprintf(fp, " %s\n", p->anno);
+			else err_fprintf(fp, "\n");
+			err_fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
+		}
+		err_fflush(fp);
+		err_fclose(fp);
+	}
+	{ // dump .amb
+		strcpy(str, prefix); strcat(str, ".amb");
+		fp = xopen(str, "w");
+		err_fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
+		for (i = 0; i != bns->n_holes; ++i) {
+			bntamb1_t *p = bns->ambs + i;
+			err_fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
+		}
+		err_fflush(fp);
+		err_fclose(fp);
+	}
+}
+
+bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
+{
+	char str[8192];
+	FILE *fp;
+	const char *fname;
+	bntseq_t *bns;
+	long long xx;
+	int i;
+	int scanres;
+	bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
+	{ // read .ann
+		fp = xopen(fname = ann_filename, "r");
+		scanres = fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
+		if (scanres != 3) goto badread;
+		bns->l_pac = xx;
+		bns->anns = (bntann1_t*)calloc(bns->n_seqs, sizeof(bntann1_t));
+		for (i = 0; i < bns->n_seqs; ++i) {
+			bntann1_t *p = bns->anns + i;
+			char *q = str;
+			int c;
+			// read gi and sequence name
+			scanres = fscanf(fp, "%u%s", &p->gi, str);
+			if (scanres != 2) goto badread;
+			p->name = strdup(str);
+			// read fasta comments 
+			while (q - str < sizeof(str) - 1 && (c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
+			while (c != '\n' && c != EOF) c = fgetc(fp);
+			if (c == EOF) {
+				scanres = EOF;
+				goto badread;
+			}
+			*q = 0;
+			if (q - str > 1 && strcmp(str, " (null)") != 0) p->anno = strdup(str + 1); // skip leading space
+			else p->anno = strdup("");
+			// read the rest
+			scanres = fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
+			if (scanres != 3) goto badread;
+			p->offset = xx;
+		}
+		err_fclose(fp);
+	}
+	{ // read .amb
+		int64_t l_pac;
+		int32_t n_seqs;
+		fp = xopen(fname = amb_filename, "r");
+		scanres = fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
+		if (scanres != 3) goto badread;
+		l_pac = xx;
+		xassert(l_pac == bns->l_pac && n_seqs == bns->n_seqs, "inconsistent .ann and .amb files.");
+		bns->ambs = bns->n_holes? (bntamb1_t*)calloc(bns->n_holes, sizeof(bntamb1_t)) : 0;
+		for (i = 0; i < bns->n_holes; ++i) {
+			bntamb1_t *p = bns->ambs + i;
+			scanres = fscanf(fp, "%lld%d%s", &xx, &p->len, str);
+			if (scanres != 3) goto badread;
+			p->offset = xx;
+			p->amb = str[0];
+		}
+		err_fclose(fp);
+	}
+	{ // open .pac
+		bns->fp_pac = xopen(pac_filename, "rb");
+	}
+	return bns;
+
+ badread:
+	if (EOF == scanres) {
+		err_fatal(__func__, "Error reading %s : %s\n", fname, ferror(fp) ? strerror(errno) : "Unexpected end of file");
+	}
+	err_fatal(__func__, "Parse error reading %s\n", fname);
+}
+
+bntseq_t *bns_restore(const char *prefix)
+{  
+	char ann_filename[1024], amb_filename[1024], pac_filename[1024], alt_filename[1024];
+	FILE *fp;
+	bntseq_t *bns;
+	strcat(strcpy(ann_filename, prefix), ".ann");
+	strcat(strcpy(amb_filename, prefix), ".amb");
+	strcat(strcpy(pac_filename, prefix), ".pac");
+	bns = bns_restore_core(ann_filename, amb_filename, pac_filename);
+	if (bns == 0) return 0;
+	if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
+		char str[1024];
+		khash_t(str) *h;
+		int c, i, absent;
+		khint_t k;
+		h = kh_init(str);
+		for (i = 0; i < bns->n_seqs; ++i) {
+			k = kh_put(str, h, bns->anns[i].name, &absent);
+			kh_val(h, k) = i;
+		}
+		i = 0;
+		while ((c = fgetc(fp)) != EOF) {
+			if (c == '\t' || c == '\n' || c == '\r') {
+				str[i] = 0;
+				if (str[0] != '@') {
+					k = kh_get(str, h, str);
+					if (k != kh_end(h))
+						bns->anns[kh_val(h, k)].is_alt = 1;
+				}
+				while (c != '\n' && c != EOF) c = fgetc(fp);
+				i = 0;
+			} else {
+				if (i >= 1022) {
+					fprintf(stderr, "[E::%s] sequence name longer than 1023 characters. Abort!\n", __func__);
+					exit(1);
+				}
+				str[i++] = c;
+			}
+		}
+		kh_destroy(str, h);
+		fclose(fp);
+	}
+	return bns;
+}
+
+void bns_destroy(bntseq_t *bns)
+{
+	if (bns == 0) return;
+	else {
+		int i;
+		if (bns->fp_pac) err_fclose(bns->fp_pac);
+		free(bns->ambs);
+		for (i = 0; i < bns->n_seqs; ++i) {
+			free(bns->anns[i].name);
+			free(bns->anns[i].anno);
+		}
+		free(bns->anns);
+		free(bns);
+	}
+}
+
+#define _set_pac(pac, l, c) ((pac)[(l)>>2] |= (c)<<((~(l)&3)<<1))
+#define _get_pac(pac, l) ((pac)[(l)>>2]>>((~(l)&3)<<1)&3)
+
+static uint8_t *add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q)
+{
+	bntann1_t *p; // 染色体，contig
+	int i, lasts;
+	if (bns->n_seqs == *m_seqs) { // 空间不够，重新开辟空间，n_seqs表示contig（染色体）数量
+		*m_seqs <<= 1;
+		bns->anns = (bntann1_t*)realloc(bns->anns, *m_seqs * sizeof(bntann1_t));
+	}
+	p = bns->anns + bns->n_seqs; // p表示当前要读入的contig
+	p->name = strdup((char*)seq->name.s); // contig名字，1,2,3... X,Y
+	p->anno = seq->comment.l > 0? strdup((char*)seq->comment.s) : strdup("(null)"); // 染色体注释，名称等信息
+	p->gi = 0; p->len = seq->seq.l; // contig长度
+	p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len; // offset表示该contig在所有序列中的偏移位置
+	p->n_ambs = 0; // 模棱两可碱基的个数
+	for (i = lasts = 0; i < seq->seq.l; ++i) { // 挨个读取该contig的碱基
+		int c = nst_nt4_table[(int)seq->seq.s[i]]; // 碱基编码
+		if (c >= 4) { // N
+			if (lasts == seq->seq.s[i]) { // contiguous N
+				++(*q)->len; // 该连续的模棱两可碱基长度+1
+			} else { // 新一串模棱两可碱基
+				if (bns->n_holes == *m_holes) { // 模棱两可碱基串容量不够，扩容
+					(*m_holes) <<= 1;
+					bns->ambs = (bntamb1_t*)realloc(bns->ambs, (*m_holes) * sizeof(bntamb1_t));
+				}
+				*q = bns->ambs + bns->n_holes;
+				(*q)->len = 1;
+				(*q)->offset = p->offset + i; // 模棱两可碱基偏移
+				(*q)->amb = seq->seq.s[i];
+				++p->n_ambs; // 该contig包括的模棱两可碱基数量
+				++bns->n_holes; // 模棱两可碱基串数量
+			}
+		}
+		lasts = seq->seq.s[i]; // 保存当前字符，用来下一轮比较
+		{ // fill buffer
+			if (c >= 4) c = lrand48()&3; // 如果是模棱两可碱基，那就随机给分配一个ATGC
+			if (bns->l_pac == *m_pac) { // double the pac size
+				*m_pac <<= 1;
+				pac = realloc(pac, *m_pac/4);
+				memset(pac + bns->l_pac/4, 0, (*m_pac - bns->l_pac)/4);
+			}
+			_set_pac(pac, bns->l_pac, c);
+			++bns->l_pac;
+		}
+	}
+	++bns->n_seqs;
+	return pac;
+}
+
+int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
+{
+	extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c
+	kseq_t *seq;
+	char name[1024];
+	bntseq_t *bns;
+	uint8_t *pac = 0;
+	int32_t m_seqs, m_holes;
+	int64_t ret = -1, m_pac, l;
+	bntamb1_t *q;
+	FILE *fp;
+
+	// initialization
+	seq = kseq_init(fp_fa);
+	bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
+	bns->seed = 11; // fixed seed for random generator
+	srand48(bns->seed);
+	m_seqs = m_holes = 8; m_pac = 0x10000;
+	bns->anns = (bntann1_t*)calloc(m_seqs, sizeof(bntann1_t));
+	bns->ambs = (bntamb1_t*)calloc(m_holes, sizeof(bntamb1_t));
+	pac = calloc(m_pac/4, 1);
+	q = bns->ambs;
+	strcpy(name, prefix); strcat(name, ".pac");
+	fp = xopen(name, "wb");
+	// read sequences
+	while (kseq_read(seq) >= 0) pac = add1(seq, bns, pac, &m_pac, &m_seqs, &m_holes, &q);
+	if (!for_only) { // add the reverse complemented sequence
+		int64_t ll_pac = (bns->l_pac * 2 + 3) / 4 * 4;
+		if (ll_pac > m_pac) pac = realloc(pac, ll_pac/4);
+		memset(pac + (bns->l_pac+3)/4, 0, (ll_pac - (bns->l_pac+3)/4*4) / 4);
+		for (l = bns->l_pac - 1; l >= 0; --l, ++bns->l_pac)
+			_set_pac(pac, bns->l_pac, 3-_get_pac(pac, l));
+	}
+	ret = bns->l_pac;
+	{ // finalize .pac file
+		ubyte_t ct;
+		err_fwrite(pac, 1, (bns->l_pac>>2) + ((bns->l_pac&3) == 0? 0 : 1), fp);
+		// the following codes make the pac file size always (l_pac/4+1+1)
+		if (bns->l_pac % 4 == 0) {
+			ct = 0;
+			err_fwrite(&ct, 1, 1, fp);
+		}
+		ct = bns->l_pac % 4;
+		err_fwrite(&ct, 1, 1, fp);
+		// close .pac file
+		err_fflush(fp);
+		err_fclose(fp);
+	}
+	bns_dump(bns, prefix);
+	bns_destroy(bns);
+	kseq_destroy(seq);
+	free(pac);
+	return ret;
+}
+
+int bwa_fa2pac(int argc, char *argv[])
+{
+	int c, for_only = 0;
+	gzFile fp;
+	while ((c = getopt(argc, argv, "f")) >= 0) {
+		switch (c) {
+			case 'f': for_only = 1; break;
+		}
+	}
+	if (argc == optind) {
+		fprintf(stderr, "Usage: bwa fa2pac [-f] <in.fasta> [<out.prefix>]\n");
+		return 1;
+	}
+	fp = xzopen(argv[optind], "r");
+	bns_fasta2bntseq(fp, (optind+1 < argc)? argv[optind+1] : argv[optind], for_only);
+	err_gzclose(fp);
+	return 0;
+}
+
+int bns_pos2rid(const bntseq_t *bns, int64_t pos_f)
+{
+	int left, mid, right;
+	if (pos_f >= bns->l_pac) return -1;
+	left = 0; mid = 0; right = bns->n_seqs;
+	while (left < right) { // binary search
+		mid = (left + right) >> 1;
+		if (pos_f >= bns->anns[mid].offset) {
+			if (mid == bns->n_seqs - 1) break;
+			if (pos_f < bns->anns[mid+1].offset) break; // bracketed
+			left = mid + 1;
+		} else right = mid;
+	}
+	return mid;
+}
+
+int bns_intv2rid(const bntseq_t *bns, int64_t rb, int64_t re)
+{
+	int is_rev, rid_b, rid_e;
+	if (rb < bns->l_pac && re > bns->l_pac) return -2;
+	assert(rb <= re);
+	rid_b = bns_pos2rid(bns, bns_depos(bns, rb, &is_rev));
+	rid_e = rb < re? bns_pos2rid(bns, bns_depos(bns, re - 1, &is_rev)) : rid_b;
+	return rid_b == rid_e? rid_b : -1;
+}
+
+int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id)
+{
+	int left, mid, right, nn;
+	if (ref_id) *ref_id = bns_pos2rid(bns, pos_f);
+	left = 0; right = bns->n_holes; nn = 0;
+	while (left < right) {
+		mid = (left + right) >> 1;
+		if (pos_f >= bns->ambs[mid].offset + bns->ambs[mid].len) left = mid + 1;
+		else if (pos_f + len <= bns->ambs[mid].offset) right = mid;
+		else { // overlap
+			if (pos_f >= bns->ambs[mid].offset) {
+				nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
+					bns->ambs[mid].offset + bns->ambs[mid].len - pos_f : len;
+			} else {
+				nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
+					bns->ambs[mid].len : len - (bns->ambs[mid].offset - pos_f);
+			}
+			break;
+		}
+	}
+	return nn;
+}
+
+uint8_t *bns_get_seq(int64_t l_pac, const uint8_t *pac, int64_t beg, int64_t end, int64_t *len)
+{
+	uint8_t *seq = 0;
+	if (end < beg) end ^= beg, beg ^= end, end ^= beg; // if end is smaller, swap
+	if (end > l_pac<<1) end = l_pac<<1;
+	if (beg < 0) beg = 0;
+	if (beg >= l_pac || end <= l_pac) {
+		int64_t k, l = 0;
+		*len = end - beg;
+		seq = malloc(end - beg);
+		if (beg >= l_pac) { // reverse strand
+			int64_t beg_f = (l_pac<<1) - 1 - end;
+			int64_t end_f = (l_pac<<1) - 1 - beg;
+			for (k = end_f; k > beg_f; --k)
+				seq[l++] = 3 - _get_pac(pac, k);
+		} else { // forward strand
+			for (k = beg; k < end; ++k)
+				seq[l++] = _get_pac(pac, k);
+		}
+	} else *len = 0; // if bridging the forward-reverse boundary, return nothing
+	return seq;
+}
+
+uint8_t *bns_fetch_seq(const bntseq_t *bns, const uint8_t *pac, int64_t *beg, int64_t mid, int64_t *end, int *rid)
+{
+	int64_t far_beg, far_end, len;
+	int is_rev;
+	uint8_t *seq;
+
+	if (*end < *beg) *end ^= *beg, *beg ^= *end, *end ^= *beg; // if end is smaller, swap
+	assert(*beg <= mid && mid < *end);
+	*rid = bns_pos2rid(bns, bns_depos(bns, mid, &is_rev));
+	far_beg = bns->anns[*rid].offset;
+	far_end = far_beg + bns->anns[*rid].len;
+	if (is_rev) { // flip to the reverse strand
+		int64_t tmp = far_beg;
+		far_beg = (bns->l_pac<<1) - far_end;
+		far_end = (bns->l_pac<<1) - tmp;
+	}
+	*beg = *beg > far_beg? *beg : far_beg;
+	*end = *end < far_end? *end : far_end;
+	seq = bns_get_seq(bns->l_pac, pac, *beg, *end, &len);
+	if (seq == 0 || *end - *beg != len) {
+		fprintf(stderr, "[E::%s] begin=%ld, mid=%ld, end=%ld, len=%ld, seq=%p, rid=%d, far_beg=%ld, far_end=%ld\n",
+				__func__, (long)*beg, (long)mid, (long)*end, (long)len, seq, *rid, (long)far_beg, (long)far_end);
+	}
+	assert(seq && *end - *beg == len); // assertion failure should never happen
+	return seq;
+}

bntseq.h

@@ -0,0 +1,92 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef BWT_BNTSEQ_H
+#define BWT_BNTSEQ_H
+
+#include <assert.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#ifndef BWA_UBYTE
+#define BWA_UBYTE
+typedef uint8_t ubyte_t;
+#endif
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	int32_t n_ambs;
+	uint32_t gi;
+	int32_t is_alt;
+	char *name, *anno;
+} bntann1_t;
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	char amb;
+} bntamb1_t;
+
+typedef struct {
+	int64_t l_pac;
+	int32_t n_seqs;
+	uint32_t seed;
+	bntann1_t *anns; // n_seqs elements 染色体
+	int32_t n_holes;
+	bntamb1_t *ambs; // n_holes elements 非AGCT字符
+	FILE *fp_pac;
+} bntseq_t;
+
+extern unsigned char nst_nt4_table[256];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void bns_dump(const bntseq_t *bns, const char *prefix);
+	bntseq_t *bns_restore(const char *prefix);
+	bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
+	void bns_destroy(bntseq_t *bns);
+	int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
+	int bns_pos2rid(const bntseq_t *bns, int64_t pos_f);
+	int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
+	uint8_t *bns_get_seq(int64_t l_pac, const uint8_t *pac, int64_t beg, int64_t end, int64_t *len);
+	uint8_t *bns_fetch_seq(const bntseq_t *bns, const uint8_t *pac, int64_t *beg, int64_t mid, int64_t *end, int *rid);
+	int bns_intv2rid(const bntseq_t *bns, int64_t rb, int64_t re);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
+{
+	return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
+}
+
+#endif

bwa.1

@@ -0,0 +1,871 @@
+.TH bwa 1 "23 October 2017" "bwa-0.7.17-r1188" "Bioinformatics tools"
+.SH NAME
+.PP
+bwa - Burrows-Wheeler Alignment Tool
+.SH SYNOPSIS
+.PP
+bwa index ref.fa
+.PP
+bwa mem ref.fa reads.fq > aln-se.sam
+.PP
+bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
+.PP
+bwa aln ref.fa short_read.fq > aln_sa.sai
+.PP
+bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam
+.PP
+bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
+.PP
+bwa bwasw ref.fa long_read.fq > aln.sam
+
+.SH DESCRIPTION
+.PP
+BWA is a software package for mapping low-divergent sequences against a large
+reference genome, such as the human genome. It consists of three algorithms:
+BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
+sequence reads up to 100bp, while the rest two for longer sequences ranged from
+70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read
+support and split alignment, but BWA-MEM, which is the latest, is generally
+recommended for high-quality queries as it is faster and more accurate.
+BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina
+reads.
+
+For all the algorithms, BWA first needs to construct the FM-index for
+the reference genome (the
+.B index
+command). Alignment algorithms are invoked with different sub-commands:
+.BR aln / samse / sampe
+for BWA-backtrack,
+.B bwasw
+for BWA-SW and
+.B mem
+for the BWA-MEM algorithm.
+
+.SH COMMANDS AND OPTIONS
+.TP
+.B index
+.B bwa index
+.RB [ -p
+.IR prefix ]
+.RB [ -a
+.IR algoType ]
+.I db.fa
+
+Index database sequences in the FASTA format.
+
+.B OPTIONS:
+.RS
+.TP 10
+.BI -p \ STR
+Prefix of the output database [same as db filename]
+.TP
+.BI -a \ STR
+Algorithm for constructing BWT index. BWA implements three algorithms for BWT
+construction:
+.BR is ,
+.B bwtsw
+and
+.BR rb2 .
+The first algorithm is a little faster for small database but requires large
+RAM and does not work for databases with total length longer than 2GB. The
+second algorithm is adapted from the BWT-SW source code. It in theory works
+with database with trillions of bases. When this option is not specified, the
+appropriate algorithm will be chosen automatically.
+.RE
+
+.TP
+.B mem
+.B bwa mem
+.RB [ -aCHjMpP ]
+.RB [ -t
+.IR nThreads ]
+.RB [ -k
+.IR minSeedLen ]
+.RB [ -w
+.IR bandWidth ]
+.RB [ -d
+.IR zDropoff ]
+.RB [ -r
+.IR seedSplitRatio ]
+.RB [ -c
+.IR maxOcc ]
+.RB [ -D
+.IR chainShadow ]
+.RB [ -m
+.IR maxMateSW ]
+.RB [ -W
+.IR minSeedMatch ]
+.RB [ -A
+.IR matchScore ]
+.RB [ -B
+.IR mmPenalty ]
+.RB [ -O
+.IR gapOpenPen ]
+.RB [ -E
+.IR gapExtPen ]
+.RB [ -L
+.IR clipPen ]
+.RB [ -U
+.IR unpairPen ]
+.RB [ -x
+.IR readType ]
+.RB [ -R
+.IR RGline ]
+.RB [ -H
+.IR HDlines ]
+.RB [ -v
+.IR verboseLevel ]
+.I db.prefix
+.I reads.fq
+.RI [ mates.fq ]
+
+Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the
+algorithm works by seeding alignments with maximal exact matches (MEMs) and
+then extending seeds with the affine-gap Smith-Waterman algorithm (SW).
+
+If
+.I mates.fq
+file is absent and option
+.B -p
+is not set, this command regards input reads are single-end. If
+.I mates.fq
+is present, this command assumes the
+.IR i -th
+read in
+.I reads.fq
+and the
+.IR i -th
+read in
+.I mates.fq
+constitute a read pair. If
+.B -p
+is used, the command assumes the
+.RI 2 i -th
+and the
+.RI (2 i +1)-th
+read in
+.I reads.fq
+constitute a read pair (such input file is said to be interleaved). In this case,
+.I mates.fq
+is ignored. In the paired-end mode, the
+.B mem
+command will infer the read orientation and the insert size distribution from a
+batch of reads.
+
+The BWA-MEM algorithm performs local alignment. It may produce multiple primary
+alignments for different part of a query sequence. This is a crucial feature
+for long sequences. However, some tools may not work with split alignments. 
+One may consider to use option
+.B -M
+to flag shorter split hits as secondary.
+
+.RS
+.TP 10
+.B ALGORITHM OPTIONS:
+.TP
+.BI -t \ INT
+Number of threads [1]
+.TP
+.BI -k \ INT
+Minimum seed length. Matches shorter than
+.I INT
+will be missed. The alignment speed is usually insensitive to this value unless
+it significantly deviates from 20. [19]
+.TP
+.BI -w \ INT
+Band width. Essentially, gaps longer than
+.I INT
+will not be found. Note that the maximum gap length is also affected by the
+scoring matrix and the hit length, not solely determined by this option. [100]
+.TP
+.BI -d \ INT
+Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between
+the best and the current extension score is above
+.RI | i - j |* A + INT ,
+where
+.I i
+and
+.I j
+are the current positions of the query and reference, respectively, and
+.I A
+is the matching score. Z-dropoff is similar to BLAST's X-dropoff except that it
+doesn't penalize gaps in one of the sequences in the alignment. Z-dropoff not
+only avoids unnecessary extension, but also reduces poor alignments inside a
+long good alignment. [100]
+.TP
+.BI -r \ FLOAT
+Trigger re-seeding for a MEM longer than
+.IR minSeedLen * FLOAT .
+This is a key heuristic parameter for tuning the performance. Larger value
+yields fewer seeds, which leads to faster alignment speed but lower accuracy. [1.5]
+.TP
+.BI -c \ INT
+Discard a MEM if it has more than
+.I INT
+occurence in the genome. This is an insensitive parameter. [500]
+.TP
+.BI -D \ FLOAT
+Drop chains shorter than
+.I FLOAT
+fraction of the longest overlapping chain [0.5]
+.TP
+.BI -m \ INT
+Perform at most
+.I INT
+rounds of mate-SW [50]
+.TP
+.BI -W \ INT
+Drop a chain if the number of bases in seeds is smaller than
+.IR INT .
+This option is primarily used for longer contigs/reads. When positive, it also
+affects seed filtering. [0]
+.TP
+.B -P
+In the paired-end mode, perform SW to rescue missing hits only but do not try to find
+hits that fit a proper pair.
+
+.TP
+.B SCORING OPTIONS:
+.TP
+.BI -A \ INT
+Matching score. [1]
+.TP
+.BI -B \ INT
+Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]
+.TP
+.BI -O \ INT[,INT]
+Gap open penalty. If two numbers are specified, the first is the penalty of
+openning a deletion and the second for openning an insertion. [6]
+.TP
+.BI -E \ INT[,INT]
+Gap extension penalty. If two numbers are specified, the first is the penalty
+of extending a deletion and second for extending an insertion. A gap of length
+k costs O + k*E (i.e.
+.B -O
+is for opening a zero-length gap). [1]
+.TP
+.BI -L \ INT[,INT]
+Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best
+score reaching the end of query. If this score is larger than the best SW score
+minus the clipping penalty, clipping will not be applied. Note that in this
+case, the SAM AS tag reports the best SW score; clipping penalty is not
+deduced. If two numbers are provided, the first is for 5'-end clipping and
+second for 3'-end clipping. [5]
+.TP
+.BI -U \ INT
+Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
+.RI scoreRead1+scoreRead2- INT
+and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these
+two scores to determine whether we should force pairing. A larger value leads to
+more aggressive read pair. [17]
+.TP
+.BI -x \ STR
+Read type. Changes multiple parameters unless overriden [null]
+.RS
+.TP 10
+.BR pacbio :
+.B -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0
+(PacBio reads to ref)
+.TP
+.BR ont2d :
+.B -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0
+(Oxford Nanopore 2D-reads to ref)
+.TP
+.BR intractg :
+.B -B9 -O16 -L5
+(intra-species contigs to ref)
+.RE
+.TP
+.B INPUT/OUTPUT OPTIONS:
+.TP
+.B -p
+Smart pairing. If two adjacent reads have the same name, they are considered
+to form a read pair. This way, paired-end and single-end reads can be mixed
+in a single FASTA/Q stream.
+.TP
+.BI -R \ STR
+Complete read group header line. '\\t' can be used in
+.I STR
+and will be converted to a TAB in the output SAM. The read group ID will be
+attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
+[null]
+.TP
+.BI -H \ ARG
+If ARG starts with @, it is interpreted as a string and gets inserted into the
+output SAM header; otherwise, ARG is interpreted as a file with all lines
+starting with @ in the file inserted into the SAM header. [null]
+.TP
+.BI -o \ FILE
+Write the output SAM file to
+.IR FILE .
+For compatibility with other BWA commands, this option may also be given as
+.B -f
+.IR FILE .
+[standard ouptut]
+.TP
+.B -q
+ Don't reduce the mapping quality of split alignment of lower alignment score.
+.TP
+.B -5
+For split alignment, mark the segment with the smallest coordinate as the
+primary. It automatically applies option
+.B -q
+as well. This option may help some Hi-C pipelines. By default, BWA-MEM marks
+highest scoring segment as primary.
+.TP
+.B -K \ INT
+Process
+.I INT
+input bases in each batch regardless of the number of threads in use
+.RI [10000000* nThreads ].
+By default, the batch size is proportional to the number of threads in use.
+Because the inferred insert size distribution slightly depends on the batch
+size, using different number of threads may produce different output.
+Specifying this option helps reproducibility.
+.TP
+.BI -T \ INT
+Don't output alignment with score lower than
+.IR INT .
+This option affects output and occasionally SAM flag 2. [30]
+.TP
+.BI -j
+Treat ALT contigs as part of the primary assembly (i.e. ignore the
+.I db.prefix.alt
+file).
+.TP
+.BI -h \ INT[,INT2]
+If a query has not more than
+.I INT
+hits with score higher than 80% of the best hit, output them all in the XA tag.
+If
+.I INT2
+is specified, BWA-MEM outputs up to
+.I INT2
+hits if the list contains a hit to an ALT contig. [5,200]
+.TP
+.B -a
+Output all found alignments for single-end or unpaired paired-end reads. These
+alignments will be flagged as secondary alignments.
+.TP
+.B -C
+Append FASTA/Q comment to SAM output. This option can be used to
+transfer read meta information (e.g. barcode) to the SAM output. Note that the
+FASTA/Q comment (the string after a space in the header line) must conform the SAM
+spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
+.TP
+.B -Y
+Use soft clipping CIGAR operation for supplementary alignments. By default, BWA-MEM
+uses soft clipping for the primary alignment and hard clipping for
+supplementary alignments.
+.TP
+.B -M
+Mark shorter split hits as secondary (for Picard compatibility).
+.TP
+.BI -v \ INT
+Control the verbosity level of the output. This option has not been fully
+supported throughout BWA. Ideally, a value 0 for disabling all the output to
+stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for
+all normal messages; 4 or higher for debugging. When this option takes value
+4, the output is not SAM. [3]
+.TP
+.BI -I \ FLOAT[,FLOAT[,INT[,INT]]]
+Specify the mean, standard deviation (10% of the mean if absent), max (4 sigma
+from the mean if absent) and min (4 sigma if absent) of the insert size
+distribution. Only applicable to the FR orientation. By default, BWA-MEM infers
+these numbers and the pair orientations given enough reads. [inferred]
+
+.RE
+
+.TP
+.B aln
+bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i
+nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc]
+[-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> >
+<out.sai>
+
+Find the SA coordinates of the input reads. Maximum
+.I maxSeedDiff
+differences are allowed in the first
+.I seedLen
+subsequence and maximum
+.I maxDiff
+differences are allowed in the whole sequence.
+
+.B OPTIONS:
+.RS
+.TP 10
+.BI -n \ NUM
+Maximum edit distance if the value is INT, or the fraction of missing
+alignments given 2% uniform base error rate if FLOAT. In the latter
+case, the maximum edit distance is automatically chosen for different
+read lengths. [0.04]
+.TP
+.BI -o \ INT
+Maximum number of gap opens [1]
+.TP
+.BI -e \ INT
+Maximum number of gap extensions, -1 for k-difference mode (disallowing
+long gaps) [-1]
+.TP
+.BI -d \ INT
+Disallow a long deletion within INT bp towards the 3'-end [16]
+.TP
+.BI -i \ INT
+Disallow an indel within INT bp towards the ends [5]
+.TP
+.BI -l \ INT
+Take the first INT subsequence as seed. If INT is larger than the query
+sequence, seeding will be disabled. For long reads, this option is
+typically ranged from 25 to 35 for `-k 2'. [inf]
+.TP
+.BI -k \ INT
+Maximum edit distance in the seed [2]
+.TP
+.BI -t \ INT
+Number of threads (multi-threading mode) [1]
+.TP
+.BI -M \ INT
+Mismatch penalty. BWA will not search for suboptimal hits with a score
+lower than (bestScore-misMsc). [3]
+.TP
+.BI -O \ INT
+Gap open penalty [11]
+.TP
+.BI -E \ INT
+Gap extension penalty [4]
+.TP
+.BI -R \ INT
+Proceed with suboptimal alignments if there are no more than INT equally
+best hits. This option only affects paired-end mapping. Increasing this
+threshold helps to improve the pairing accuracy at the cost of speed,
+especially for short reads (~32bp).
+.TP
+.B -c
+Reverse query but not complement it, which is required for alignment in
+the color space. (Disabled since 0.6.x)
+.TP
+.B -N
+Disable iterative search. All hits with no more than
+.I maxDiff
+differences will be found. This mode is much slower than the default.
+.TP
+.BI -q \ INT
+Parameter for read trimming. BWA trims a read down to
+argmax_x{\\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original
+read length. [0]
+.TP
+.B -I
+The input is in the Illumina 1.3+ read format (quality equals ASCII-64).
+.TP
+.BI -B \ INT
+Length of barcode starting from the 5'-end. When
+.I INT
+is positive, the barcode of each read will be trimmed before mapping and will
+be written at the
+.B BC
+SAM tag. For paired-end reads, the barcode from both ends are concatenated. [0]
+.TP
+.B -b
+Specify the input read sequence file is the BAM format. For paired-end
+data, two ends in a pair must be grouped together and options
+.B -1
+or
+.B -2
+are usually applied to specify which end should be mapped. Typical
+command lines for mapping pair-end data in the BAM format are:
+
+    bwa aln ref.fa -b1 reads.bam > 1.sai
+    bwa aln ref.fa -b2 reads.bam > 2.sai
+    bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
+.TP
+.B -0
+When
+.B -b
+is specified, only use single-end reads in mapping.
+.TP
+.B -1
+When
+.B -b
+is specified, only use the first read in a read pair in mapping (skip
+single-end reads and the second reads).
+.TP
+.B -2
+When
+.B -b
+is specified, only use the second read in a read pair in mapping.
+.B
+.RE
+
+.TP
+.B samse
+bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>
+
+Generate alignments in the SAM format given single-end reads. Repetitive
+hits will be randomly chosen.
+
+.B OPTIONS:
+.RS
+.TP 10
+.BI -n \ INT
+Maximum number of alignments to output in the XA tag for reads paired
+properly. If a read has more than INT hits, the XA tag will not be
+written. [3]
+.TP
+.BI -r \ STR
+Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
+.RE
+
+.TP
+.B sampe
+bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis]
+[-P] <in.db.fasta> <in1.sai> <in2.sai> <in1.fq> <in2.fq> > <out.sam>
+
+Generate alignments in the SAM format given paired-end reads. Repetitive
+read pairs will be placed randomly.
+
+.B OPTIONS:
+.RS
+.TP 8
+.BI -a \ INT
+Maximum insert size for a read pair to be considered being mapped
+properly. Since 0.4.5, this option is only used when there are not
+enough good alignment to infer the distribution of insert sizes. [500]
+.TP
+.BI -o \ INT
+Maximum occurrences of a read for pairing. A read with more occurrneces
+will be treated as a single-end read. Reducing this parameter helps
+faster pairing. [100000]
+.TP
+.B -P
+Load the entire FM-index into memory to reduce disk operations
+(base-space reads only). With this option, at least 1.25N bytes of
+memory are required, where N is the length of the genome.
+.TP
+.BI -n \ INT
+Maximum number of alignments to output in the XA tag for reads paired
+properly. If a read has more than INT hits, the XA tag will not be
+written. [3]
+.TP
+.BI -N \ INT
+Maximum number of alignments to output in the XA tag for disconcordant
+read pairs (excluding singletons). If a read has more than INT hits, the
+XA tag will not be written. [10]
+.TP
+.BI -r \ STR
+Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
+.RE
+
+.TP
+.B bwasw
+bwa bwasw [-a matchScore] [-b mmPen] [-q gapOpenPen] [-r gapExtPen] [-t
+nThreads] [-w bandWidth] [-T thres] [-s hspIntv] [-z zBest] [-N
+nHspRev] [-c thresCoef] <in.db.fasta> <in.fq> [mate.fq]
+
+Align query sequences in the
+.I in.fq
+file. When
+.I mate.fq
+is present, perform paired-end alignment. The paired-end mode only works
+for reads Illumina short-insert libraries. In the paired-end mode, BWA-SW
+may still output split alignments but they are all marked as not properly
+paired; the mate positions will not be written if the mate has multiple
+local hits.
+
+.B OPTIONS:
+.RS
+.TP 10
+.BI -a \ INT
+Score of a match [1]
+.TP
+.BI -b \ INT
+Mismatch penalty [3]
+.TP
+.BI -q \ INT
+Gap open penalty [5]
+.TP
+.BI -r \ INT
+Gap extension penalty. The penalty for a contiguous gap of size k is
+q+k*r. [2]
+.TP
+.BI -t \ INT
+Number of threads in the multi-threading mode [1]
+.TP
+.BI -w \ INT
+Band width in the banded alignment [33]
+.TP
+.BI -T \ INT
+Minimum score threshold divided by a [37]
+.TP
+.BI -c \ FLOAT
+Coefficient for threshold adjustment according to query length. Given an
+l-long query, the threshold for a hit to be retained is
+a*max{T,c*log(l)}. [5.5]
+.TP
+.BI -z \ INT
+Z-best heuristics. Higher -z increases accuracy at the cost of speed. [1]
+.TP
+.BI -s \ INT
+Maximum SA interval size for initiating a seed. Higher -s increases
+accuracy at the cost of speed. [3]
+.TP
+.BI -N \ INT
+Minimum number of seeds supporting the resultant alignment to skip
+reverse alignment. [5]
+.RE
+
+.SH SAM ALIGNMENT FORMAT
+.PP
+The output of the
+.B `aln'
+command is binary and designed for BWA use only. BWA outputs the final
+alignment in the SAM (Sequence Alignment/Map) format. Each line consists
+of:
+
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col	Field	Description
+_
+1	QNAME	Query (pair) NAME
+2	FLAG	bitwise FLAG
+3	RNAME	Reference sequence NAME
+4	POS	1-based leftmost POSition/coordinate of clipped sequence
+5	MAPQ	MAPping Quality (Phred-scaled)
+6	CIAGR	extended CIGAR string
+7	MRNM	Mate Reference sequence NaMe (`=' if same as RNAME)
+8	MPOS	1-based Mate POSistion
+9	ISIZE	Inferred insert SIZE
+10	SEQ	query SEQuence on the same strand as the reference
+11	QUAL	query QUALity (ASCII-33 gives the Phred base quality)
+12	OPT	variable OPTional fields in the format TAG:VTYPE:VALUE
+.TE
+
+.PP
+Each bit in the FLAG field is defined as:
+
+.TS
+center box;
+cb | cb | cb
+c | l | l .
+Chr	Flag	Description
+_
+p	0x0001	the read is paired in sequencing
+P	0x0002	the read is mapped in a proper pair
+u	0x0004	the query sequence itself is unmapped
+U	0x0008	the mate is unmapped
+r	0x0010	strand of the query (1 for reverse)
+R	0x0020	strand of the mate
+1	0x0040	the read is the first read in a pair
+2	0x0080	the read is the second read in a pair
+s	0x0100	the alignment is not primary
+f	0x0200	QC failure
+d	0x0400	optical or PCR duplicate
+S	0x0800	supplementary alignment
+.TE
+
+.PP
+The Please check <http://samtools.sourceforge.net> for the format
+specification and the tools for post-processing the alignment.
+
+BWA generates the following optional fields. Tags starting with `X' are
+specific to BWA.
+
+.TS
+center box;
+cb | cb
+cB | l .
+Tag	Meaning
+_
+NM	Edit distance
+MD	Mismatching positions/bases
+AS	Alignment score
+BC	Barcode sequence
+SA	Supplementary alignments
+_
+X0	Number of best hits
+X1	Number of suboptimal hits found by BWA
+XN	Number of ambiguous bases in the referenece
+XM	Number of mismatches in the alignment
+XO	Number of gap opens
+XG	Number of gap extentions
+XT	Type: Unique/Repeat/N/Mate-sw
+XA	Alternative hits; format: /(chr,pos,CIGAR,NM;)*/
+_
+XS	Suboptimal alignment score
+XF	Support from forward/reverse alignment
+XE	Number of supporting seeds
+.TE
+
+.PP
+Note that XO and XG are generated by BWT search while the CIGAR string
+by Smith-Waterman alignment. These two tags may be inconsistent with the
+CIGAR string. This is not a bug.
+
+.SH NOTES ON SHORT-READ ALIGNMENT
+.SS Alignment Accuracy
+.PP
+When seeding is disabled, BWA guarantees to find an alignment
+containing maximum
+.I maxDiff
+differences including
+.I maxGapO
+gap opens which do not occur within
+.I nIndelEnd
+bp towards either end of the query. Longer gaps may be found if
+.I maxGapE
+is positive, but it is not guaranteed to find all hits. When seeding is
+enabled, BWA further requires that the first
+.I seedLen
+subsequence contains no more than
+.I maxSeedDiff
+differences.
+.PP
+When gapped alignment is disabled, BWA is expected to generate the same
+alignment as Eland version 1, the Illumina alignment program. However, as BWA
+change `N' in the database sequence to random nucleotides, hits to these
+random sequences will also be counted. As a consequence, BWA may mark a
+unique hit as a repeat, if the random sequences happen to be identical
+to the sequences which should be unqiue in the database.
+.PP
+By default, if the best hit is not highly repetitive (controlled by -R), BWA
+also finds all hits contains one more mismatch; otherwise, BWA finds all
+equally best hits only. Base quality is NOT considered in evaluating
+hits. In the paired-end mode, BWA pairs all hits it found. It further
+performs Smith-Waterman alignment for unmapped reads to rescue reads with a
+high erro rate, and for high-quality anomalous pairs to fix potential alignment
+errors.
+
+.SS Estimating Insert Size Distribution
+.PP
+BWA estimates the insert size distribution per 256*1024 read pairs. It
+first collects pairs of reads with both ends mapped with a single-end
+quality 20 or higher and then calculates median (Q2), lower and higher
+quartile (Q1 and Q3). It estimates the mean and the variance of the
+insert size distribution from pairs whose insert sizes are within
+interval [Q1-2(Q3-Q1), Q3+2(Q3-Q1)]. The maximum distance x for a pair
+considered to be properly paired (SAM flag 0x2) is calculated by solving
+equation Phi((x-mu)/sigma)=x/L*p0, where mu is the mean, sigma is the
+standard error of the insert size distribution, L is the length of the
+genome, p0 is prior of anomalous pair and Phi() is the standard
+cumulative distribution function. For mapping Illumina short-insert
+reads to the human genome, x is about 6-7 sigma away from the
+mean. Quartiles, mean, variance and x will be printed to the standard
+error output.
+
+.SS Memory Requirement
+.PP
+With bwtsw algorithm, 5GB memory is required for indexing the complete
+human genome sequences. For short reads, the
+.B aln
+command uses ~3.2GB memory and the
+.B sampe
+command uses ~5.4GB.
+
+.SS Speed
+.PP
+Indexing the human genome sequences takes 3 hours with bwtsw
+algorithm. Indexing smaller genomes with IS algorithms is
+faster, but requires more memory.
+.PP
+The speed of alignment is largely determined by the error rate of the query
+sequences (r). Firstly, BWA runs much faster for near perfect hits than
+for hits with many differences, and it stops searching for a hit with
+l+2 differences if a l-difference hit is found. This means BWA will be
+very slow if r is high because in this case BWA has to visit hits with
+many differences and looking for these hits is expensive. Secondly, the
+alignment algorithm behind makes the speed sensitive to [k log(N)/m],
+where k is the maximum allowed differences, N the size of database and m
+the length of a query. In practice, we choose k w.r.t. r and therefore r
+is the leading factor. I would not recommend to use BWA on data with
+r>0.02.
+.PP
+Pairing is slower for shorter reads. This is mainly because shorter
+reads have more spurious hits and converting SA coordinates to
+chromosomal coordinates are very costly.
+
+.SH CHANGES IN BWA-0.6
+.PP
+Since version 0.6, BWA has been able to work with a reference genome longer than 4GB.
+This feature makes it possible to integrate the forward and reverse complemented
+genome in one FM-index, which speeds up both BWA-short and BWA-SW. As a tradeoff,
+BWA uses more memory because it has to keep all positions and ranks in 64-bit
+integers, twice larger than 32-bit integers used in the previous versions.
+
+The latest BWA-SW also works for paired-end reads longer than 100bp. In
+comparison to BWA-short, BWA-SW tends to be more accurate for highly unique
+reads and more robust to relative long INDELs and structural variants.
+Nonetheless, BWA-short usually has higher power to distinguish the optimal hit
+from many suboptimal hits. The choice of the mapping algorithm may depend on
+the application.
+
+.SH SEE ALSO
+BWA website <http://bio-bwa.sourceforge.net>, Samtools website
+<http://samtools.sourceforge.net>
+
+.SH AUTHOR
+Heng Li at the Sanger Institute wrote the key source codes and
+integrated the following codes for BWT construction: bwtsw
+<http://i.cs.hku.hk/~ckwong3/bwtsw/>, implemented by Chi-Kwong Wong at
+the University of Hong Kong and IS
+<http://yuta.256.googlepages.com/sais> originally proposed by Nong Ge
+<http://www.cs.sysu.edu.cn/nong/> at the Sun Yat-Sen University and
+implemented by Yuta Mori.
+
+.SH LICENSE AND CITATION
+.PP
+The full BWA package is distributed under GPLv3 as it uses source codes
+from BWT-SW which is covered by GPL. Sorting, hash table, BWT and IS
+libraries are distributed under the MIT license.
+.PP
+If you use the BWA-backtrack algorithm, please cite the following
+paper:
+.PP
+Li H. and Durbin R. (2009) Fast and accurate short read alignment with
+Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
+.PP
+If you use the BWA-SW algorithm, please cite:
+.PP
+Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
+Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]
+.PP
+If you use BWA-MEM or the fastmap component of BWA, please cite:
+.PP
+Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with
+BWA-MEM. arXiv:1303.3997v1 [q-bio.GN].
+.PP
+It is likely that the BWA-MEM manuscript will not appear in a peer-reviewed
+journal.
+
+.SH HISTORY
+BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW
+and mimics its binary file formats; BWA-SW resembles BWT-SW in several
+ways. The initial idea about BWT-based alignment also came from the
+group who developed BWT-SW. At the same time, BWA is different enough
+from BWT-SW. The short-read alignment algorithm bears no similarity to
+Smith-Waterman algorithm any more. While BWA-SW learns from BWT-SW, it
+introduces heuristics that can hardly be applied to the original
+algorithm. In all, BWA does not guarantee to find all local hits as what
+BWT-SW is designed to do, but it is much faster than BWT-SW on both
+short and long query sequences.
+
+I started to write the first piece of codes on 24 May 2008 and got the
+initial stable version on 02 June 2008. During this period, I was
+acquainted that Professor Tak-Wah Lam, the first author of BWT-SW paper,
+was collaborating with Beijing Genomics Institute on SOAP2, the successor
+to SOAP (Short Oligonucleotide Analysis Package). SOAP2 has come out in
+November 2008. According to the SourceForge download page, the third
+BWT-based short read aligner, bowtie, was first released in August
+2008. At the time of writing this manual, at least three more BWT-based
+short-read aligners are being implemented.
+
+The BWA-SW algorithm is a new component of BWA. It was conceived in
+November 2008 and implemented ten months later.
+
+The BWA-MEM algorithm is based on an algorithm finding super-maximal exact
+matches (SMEMs), which was first published with the fermi assembler paper
+in 2012. I first implemented the basic SMEM algorithm in the
+.B fastmap
+command for an experiment and then extended the basic algorithm and added the
+extension part in Feburary 2013 to make BWA-MEM a fully featured mapper.
+

bwa.c

@@ -0,0 +1,501 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <assert.h>
+#include "bntseq.h"
+#include "bwa.h"
+#include "ksw.h"
+#include "utils.h"
+#include "kstring.h"
+#include "kvec.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+int bwa_verbose = 3;
+int bwa_dbg = 0;
+char bwa_rg_id[256];
+char *bwa_pg;
+
+/************************
+ * Batch FASTA/Q reader *
+ ************************/
+
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+static inline void trim_readno(kstring_t *s)
+{
+	if (s->l > 2 && s->s[s->l-2] == '/' && isdigit(s->s[s->l-1]))
+		s->l -= 2, s->s[s->l] = 0;
+}
+
+static inline char *dupkstring(const kstring_t *str, int dupempty)
+{
+	char *s = (str->l > 0 || dupempty)? malloc(str->l + 1) : NULL;
+	if (!s) return NULL;
+
+	memcpy(s, str->s, str->l);
+	s[str->l] = '\0';
+	return s;
+}
+
+static inline void kseq2bseq1(const kseq_t *ks, bseq1_t *s)
+{ // TODO: it would be better to allocate one chunk of memory, but probably it does not matter in practice
+	s->name = dupkstring(&ks->name, 1);
+	s->comment = dupkstring(&ks->comment, 0);
+	s->seq = dupkstring(&ks->seq, 1);
+	s->qual = dupkstring(&ks->qual, 0);
+	s->l_seq = ks->seq.l;
+}
+
+bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
+{
+	kseq_t *ks = (kseq_t*)ks1_, *ks2 = (kseq_t*)ks2_;
+	int size = 0, m, n;
+	bseq1_t *seqs;
+	m = n = 0; seqs = 0;
+	while (kseq_read(ks) >= 0) {
+		if (ks2 && kseq_read(ks2) < 0) { // the 2nd file has fewer reads
+			fprintf(stderr, "[W::%s] the 2nd file has fewer sequences.\n", __func__);
+			break;
+		}
+		if (n >= m) {
+			m = m? m<<1 : 256;
+			seqs = realloc(seqs, m * sizeof(bseq1_t));
+		}
+		trim_readno(&ks->name);
+		kseq2bseq1(ks, &seqs[n]);
+		seqs[n].id = n;
+		size += seqs[n++].l_seq;
+		if (ks2) {
+			trim_readno(&ks2->name);
+			kseq2bseq1(ks2, &seqs[n]);
+			seqs[n].id = n;
+			size += seqs[n++].l_seq;
+		}
+		if (size >= chunk_size && (n&1) == 0) break;
+	}
+	if (size == 0) { // test if the 2nd file is finished
+		if (ks2 && kseq_read(ks2) >= 0)
+			fprintf(stderr, "[W::%s] the 1st file has fewer sequences.\n", __func__);
+	}
+	*n_ = n;
+	return seqs;
+}
+
+void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2])
+{
+	int i, has_last;
+	kvec_t(bseq1_t) a[2] = {{0,0,0}, {0,0,0}};
+	for (i = 1, has_last = 1; i < n; ++i) {
+		if (has_last) {
+			if (strcmp(seqs[i].name, seqs[i-1].name) == 0) {
+				kv_push(bseq1_t, a[1], seqs[i-1]);
+				kv_push(bseq1_t, a[1], seqs[i]);
+				has_last = 0;
+			} else kv_push(bseq1_t, a[0], seqs[i-1]);
+		} else has_last = 1;
+	}
+	if (has_last) kv_push(bseq1_t, a[0], seqs[i-1]);
+	sep[0] = a[0].a, m[0] = a[0].n;
+	sep[1] = a[1].a, m[1] = a[1].n;
+}
+
+/*****************
+ * CIGAR related *
+ *****************/
+
+void bwa_fill_scmat(int a, int b, int8_t mat[25])
+{
+	int i, j, k;
+	for (i = k = 0; i < 4; ++i) {
+		for (j = 0; j < 4; ++j)
+			mat[k++] = i == j? a : -b;
+		mat[k++] = -1; // ambiguous base
+	}
+	for (j = 0; j < 5; ++j) mat[k++] = -1;
+}
+
+// Generate CIGAR when the alignment end points are known
+uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
+{
+	uint32_t *cigar = 0;
+	uint8_t tmp, *rseq;
+	int i;
+	int64_t rlen;
+	kstring_t str;
+	const char *int2base;
+
+	if (n_cigar) *n_cigar = 0;
+	if (NM) *NM = -1;
+	if (l_query <= 0 || rb >= re || (rb < l_pac && re > l_pac)) return 0; // reject if negative length or bridging the forward and reverse strand
+	rseq = bns_get_seq(l_pac, pac, rb, re, &rlen);
+	if (re - rb != rlen) goto ret_gen_cigar; // possible if out of range
+	if (rb >= l_pac) { // then reverse both query and rseq; this is to ensure indels to be placed at the leftmost position
+		for (i = 0; i < l_query>>1; ++i)
+			tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;
+		for (i = 0; i < rlen>>1; ++i)
+			tmp = rseq[i], rseq[i] = rseq[rlen - 1 - i], rseq[rlen - 1 - i] = tmp;
+	}
+	if (l_query == re - rb && w_ == 0) { // no gap; no need to do DP
+		// UPDATE: we come to this block now... FIXME: due to an issue in mem_reg2aln(), we never come to this block. This does not affect accuracy, but it hurts performance.
+		if (n_cigar) {
+			cigar = malloc(4);
+			cigar[0] = l_query<<4 | 0;
+			*n_cigar = 1;
+		}
+		for (i = 0, *score = 0; i < l_query; ++i)
+			*score += mat[rseq[i]*5 + query[i]];
+	} else {
+		int w, max_gap, max_ins, max_del, min_w;
+		// set the band-width
+		max_ins = (int)((double)(((l_query+1)>>1) * mat[0] - o_ins) / e_ins + 1.);
+		max_del = (int)((double)(((l_query+1)>>1) * mat[0] - o_del) / e_del + 1.);
+		max_gap = max_ins > max_del? max_ins : max_del;
+		max_gap = max_gap > 1? max_gap : 1;
+		w = (max_gap + abs((int)rlen - l_query) + 1) >> 1;
+		w = w < w_? w : w_;
+		min_w = abs((int)rlen - l_query) + 3;
+		w = w > min_w? w : min_w;
+		// NW alignment
+		if (bwa_verbose >= 4) {
+			printf("* Global bandwidth: %d\n", w);
+			printf("* Global ref:   "); for (i = 0; i < rlen; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
+			printf("* Global query: "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
+		}
+		*score = ksw_global2(l_query, query, rlen, rseq, 5, mat, o_del, e_del, o_ins, e_ins, w, n_cigar, &cigar);
+	}
+	if (NM && n_cigar) {// compute NM and MD
+		int k, x, y, u, n_mm = 0, n_gap = 0;
+		str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR
+		int2base = rb < l_pac? "ACGTN" : "TGCAN";
+		for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {
+			int op, len;
+			cigar = (uint32_t*)str.s;
+			op  = cigar[k]&0xf, len = cigar[k]>>4;
+			if (op == 0) { // match
+				for (i = 0; i < len; ++i) {
+					if (query[x + i] != rseq[y + i]) {
+						kputw(u, &str);
+						kputc(int2base[rseq[y+i]], &str);
+						++n_mm; u = 0;
+					} else ++u;
+				}
+				x += len; y += len;
+			} else if (op == 2) { // deletion
+				if (k > 0 && k < *n_cigar - 1) { // don't do the following if D is the first or the last CIGAR
+					kputw(u, &str); kputc('^', &str);
+					for (i = 0; i < len; ++i)
+						kputc(int2base[rseq[y+i]], &str);
+					u = 0; n_gap += len;
+				}
+				y += len;
+			} else if (op == 1) x += len, n_gap += len; // insertion
+		}
+		kputw(u, &str); kputc(0, &str);
+		*NM = n_mm + n_gap;
+		cigar = (uint32_t*)str.s;
+	}
+	if (rb >= l_pac) // reverse back query
+		for (i = 0; i < l_query>>1; ++i)
+			tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;
+
+ret_gen_cigar:
+	free(rseq);
+	return cigar;
+}
+
+uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
+{
+	return bwa_gen_cigar2(mat, q, r, q, r, w_, l_pac, pac, l_query, query, rb, re, score, n_cigar, NM);
+}
+
+/*********************
+ * Full index reader *
+ *********************/
+
+char *bwa_idx_infer_prefix(const char *hint)
+{
+	char *prefix;
+	int l_hint;
+	FILE *fp;
+	l_hint = strlen(hint);
+	prefix = malloc(l_hint + 3 + 4 + 1);
+	strcpy(prefix, hint);
+	strcpy(prefix + l_hint, ".64.bwt");
+	if ((fp = fopen(prefix, "rb")) != 0) {
+		fclose(fp);
+		prefix[l_hint + 3] = 0;
+		return prefix;
+	} else {
+		strcpy(prefix + l_hint, ".bwt");
+		if ((fp = fopen(prefix, "rb")) == 0) {
+			free(prefix);
+			return 0;
+		} else {
+			fclose(fp);
+			prefix[l_hint] = 0;
+			return prefix;
+		}
+	}
+}
+
+bwt_t *bwa_idx_load_bwt(const char *hint)
+{
+	char *tmp, *prefix;
+	bwt_t *bwt;
+	prefix = bwa_idx_infer_prefix(hint);
+	if (prefix == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
+		return 0;
+	}
+	tmp = calloc(strlen(prefix) + 5, 1);
+	strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
+	bwt = bwt_restore_bwt(tmp);
+	strcat(strcpy(tmp, prefix), ".sa");  // partial suffix array (SA)
+	bwt_restore_sa(tmp, bwt);
+	free(tmp); free(prefix);
+	return bwt;
+}
+
+bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which)
+{
+	bwaidx_t *idx;
+	char *prefix;
+	prefix = bwa_idx_infer_prefix(hint);
+	if (prefix == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
+		return 0;
+	}
+	idx = calloc(1, sizeof(bwaidx_t));
+	if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
+	if (which & BWA_IDX_BNS) {
+		int i, c;
+		idx->bns = bns_restore(prefix);
+		for (i = c = 0; i < idx->bns->n_seqs; ++i)
+			if (idx->bns->anns[i].is_alt) ++c;
+		if (bwa_verbose >= 3)
+			fprintf(stderr, "[M::%s] read %d ALT contigs\n", __func__, c);
+		if (which & BWA_IDX_PAC) {
+			idx->pac = calloc(idx->bns->l_pac/4+1, 1);
+			err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
+			err_fclose(idx->bns->fp_pac);
+			idx->bns->fp_pac = 0;
+		}
+	}
+	free(prefix);
+	return idx;
+}
+
+bwaidx_t *bwa_idx_load(const char *hint, int which)
+{
+	return bwa_idx_load_from_disk(hint, which);
+}
+
+void bwa_idx_destroy(bwaidx_t *idx)
+{
+	if (idx == 0) return;
+	if (idx->mem == 0) {
+		if (idx->bwt) bwt_destroy(idx->bwt);
+		if (idx->bns) bns_destroy(idx->bns);
+		if (idx->pac) free(idx->pac);
+	} else {
+		free(idx->bwt); free(idx->bns->anns); free(idx->bns);
+		if (!idx->is_shm) free(idx->mem);
+	}
+	free(idx);
+}
+
+int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
+{
+	int64_t k = 0, x;
+	int i;
+
+	// generate idx->bwt
+	x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;
+	x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;
+	x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
+
+	// generate idx->bns and idx->pac
+	x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;
+	x = idx->bns->n_holes * sizeof(bntamb1_t); idx->bns->ambs = (bntamb1_t*)(mem + k); k += x;
+	x = idx->bns->n_seqs  * sizeof(bntann1_t); idx->bns->anns = malloc(x); memcpy(idx->bns->anns, mem + k, x); k += x;
+	for (i = 0; i < idx->bns->n_seqs; ++i) {
+		idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;
+		idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;
+	}
+	idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
+	assert(k == l_mem);
+
+	idx->l_mem = k; idx->mem = mem;
+	return 0;
+}
+
+int bwa_idx2mem(bwaidx_t *idx)
+{
+	int i;
+	int64_t k, x, tmp;
+	uint8_t *mem;
+
+	// copy idx->bwt
+	x = idx->bwt->bwt_size * 4;
+	mem = realloc(idx->bwt->bwt, sizeof(bwt_t) + x); idx->bwt->bwt = 0;
+	memmove(mem + sizeof(bwt_t), mem, x);
+	memcpy(mem, idx->bwt, sizeof(bwt_t)); k = sizeof(bwt_t) + x;
+	x = idx->bwt->n_sa * sizeof(bwtint_t); mem = realloc(mem, k + x); memcpy(mem + k, idx->bwt->sa, x); k += x;
+	free(idx->bwt->sa);
+	free(idx->bwt); idx->bwt = 0;
+
+	// copy idx->bns
+	tmp = idx->bns->n_seqs * sizeof(bntann1_t) + idx->bns->n_holes * sizeof(bntamb1_t);
+	for (i = 0; i < idx->bns->n_seqs; ++i) // compute the size of heap-allocated memory
+		tmp += strlen(idx->bns->anns[i].name) + strlen(idx->bns->anns[i].anno) + 2;
+	mem = realloc(mem, k + sizeof(bntseq_t) + tmp);
+	x = sizeof(bntseq_t); memcpy(mem + k, idx->bns, x); k += x;
+	x = idx->bns->n_holes * sizeof(bntamb1_t); memcpy(mem + k, idx->bns->ambs, x); k += x;
+	free(idx->bns->ambs);
+	x = idx->bns->n_seqs * sizeof(bntann1_t); memcpy(mem + k, idx->bns->anns, x); k += x;
+	for (i = 0; i < idx->bns->n_seqs; ++i) {
+		x = strlen(idx->bns->anns[i].name) + 1; memcpy(mem + k, idx->bns->anns[i].name, x); k += x;
+		x = strlen(idx->bns->anns[i].anno) + 1; memcpy(mem + k, idx->bns->anns[i].anno, x); k += x;
+		free(idx->bns->anns[i].name); free(idx->bns->anns[i].anno);
+	}
+	free(idx->bns->anns);
+
+	// copy idx->pac
+	x = idx->bns->l_pac/4+1;
+	mem = realloc(mem, k + x);
+	memcpy(mem + k, idx->pac, x); k += x;
+	free(idx->bns); idx->bns = 0;
+	free(idx->pac); idx->pac = 0;
+
+	return bwa_mem2idx(k, mem, idx);
+}
+
+/***********************
+ * SAM header routines *
+ ***********************/
+
+void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
+{
+	int i, n_HD = 0, n_SQ = 0;
+	extern char *bwa_pg;
+	
+	if (hdr_line) {
+		// check for HD line
+		const char *p = hdr_line;
+		if ((p = strstr(p, "@HD")) != 0) {
+			++n_HD;
+		}	
+		// check for SQ lines
+		p = hdr_line;
+		while ((p = strstr(p, "@SQ\t")) != 0) {
+			if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
+			p += 4;
+		}
+	}
+	if (n_SQ == 0) {
+		for (i = 0; i < bns->n_seqs; ++i) {
+			err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);
+			if (bns->anns[i].is_alt) err_printf("\tAH:*\n");
+			else err_fputc('\n', stdout);
+		}
+	} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
+		fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
+	if (n_HD == 0) {
+		err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
+	}
+	if (hdr_line) err_printf("%s\n", hdr_line);
+	if (bwa_pg) err_printf("%s\n", bwa_pg);
+}
+
+static char *bwa_escape(char *s)
+{
+	char *p, *q;
+	for (p = q = s; *p; ++p) {
+		if (*p == '\\') {
+			++p;
+			if (*p == 't') *q++ = '\t';
+			else if (*p == 'n') *q++ = '\n';
+			else if (*p == 'r') *q++ = '\r';
+			else if (*p == '\\') *q++ = '\\';
+		} else *q++ = *p;
+	}
+	*q = '\0';
+	return s;
+}
+
+char *bwa_set_rg(const char *s)
+{
+	char *p, *q, *r, *rg_line = 0;
+	memset(bwa_rg_id, 0, 256);
+	if (strstr(s, "@RG") != s) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
+		goto err_set_rg;
+	}
+	if (strstr(s, "\t") != NULL) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);
+		goto err_set_rg;
+	}
+	rg_line = strdup(s);
+	bwa_escape(rg_line);
+	if ((p = strstr(rg_line, "\tID:")) == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);
+		goto err_set_rg;
+	}
+	p += 4;
+	for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
+	if (q - p + 1 > 256) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);
+		goto err_set_rg;
+	}
+	for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
+		*r++ = *q;
+	return rg_line;
+
+err_set_rg:
+	free(rg_line);
+	return 0;
+}
+
+char *bwa_insert_header(const char *s, char *hdr)
+{
+	int len = 0;
+	if (s == 0 || s[0] != '@') return hdr;
+	if (hdr) {
+		len = strlen(hdr);
+		hdr = realloc(hdr, len + strlen(s) + 2);
+		hdr[len++] = '\n';
+		strcpy(hdr + len, s);
+	} else hdr = strdup(s);
+	bwa_escape(hdr + len);
+	return hdr;
+}

bwa.h

@@ -0,0 +1,97 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#ifndef BWA_H_
+#define BWA_H_
+
+#include <stdint.h>
+#include "bntseq.h"
+#include "bwt.h"
+
+#define BWA_IDX_BWT 0x1
+#define BWA_IDX_BNS 0x2
+#define BWA_IDX_PAC 0x4
+#define BWA_IDX_ALL 0x7
+
+#define BWA_CTL_SIZE 0x10000
+
+#define BWTALGO_AUTO  0
+#define BWTALGO_RB2   1
+#define BWTALGO_BWTSW 2
+#define BWTALGO_IS    3
+
+#define BWA_DBG_QNAME 0x1
+
+typedef struct {
+	bwt_t    *bwt; // FM-index
+	bntseq_t *bns; // information on the reference sequences
+	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
+
+	int    is_shm;
+	int64_t l_mem;
+	uint8_t  *mem;
+} bwaidx_t;
+
+typedef struct {
+	int l_seq, id;
+	char *name, *comment, *seq, *qual, *sam;
+} bseq1_t;
+
+extern int bwa_verbose, bwa_dbg;
+extern char bwa_rg_id[256];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
+	void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2]);
+
+	void bwa_fill_scmat(int a, int b, int8_t mat[25]);
+	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
+	uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
+
+	int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_size);
+
+	char *bwa_idx_infer_prefix(const char *hint);
+	bwt_t *bwa_idx_load_bwt(const char *hint);
+
+	bwaidx_t *bwa_idx_load_from_shm(const char *hint);
+	bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which);
+	bwaidx_t *bwa_idx_load(const char *hint, int which);
+	void bwa_idx_destroy(bwaidx_t *idx);
+	int bwa_idx2mem(bwaidx_t *idx);
+	int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx);
+
+	void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line);
+	char *bwa_set_rg(const char *s);
+	char *bwa_insert_header(const char *s, char *hdr);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwakit/README.md

@@ -0,0 +1,115 @@
+## Introduction
+
+Bwakit is a self-consistent installation-free package of scripts and precompiled
+binaries, providing an end-to-end solution to read mapping. In addition to the
+basic mapping functionality implemented in bwa, bwakit is able to generate
+proper human reference genome and to take advantage of ALT contigs, if present,
+to improve read mapping and to perform HLA typing for high-coverage human data.
+It can remap name- or coordinate-sorted BAM with read group and barcode
+information retained. Bwakit also *optionally* trims adapters (via
+[trimadap][ta]), marks duplicates (via [samblaster][sb]) and sorts the final
+alignment (via [samtools][smtl]).
+
+Bwakit has two entry scripts: `run-gen-ref` which downloads and generates human
+reference genomes, and `run-bwamem` which prints mapping command lines on the
+standard output that can be piped to `sh` to execute. The two scripts will call
+other programs or use data in `bwa.kit`. The following shows an example about
+how to use bwakit:
+
+```sh
+# Download the bwa-0.7.11 binary package (download link may change)
+wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2/download \
+  | gzip -dc | tar xf -
+# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
+bwa.kit/run-gen-ref hs38DH   # download GRCh38 and write hs38DH.fa
+bwa.kit/bwa index hs38DH.fa  # create BWA index
+# mapping
+bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh
+```
+
+The last mapping command line will generate the following files:
+
+* `out.aln.bam`: unsorted alignments with ALT-aware mapping quality. In this
+  file, one read may be placed on multiple overlapping ALT contigs at the same
+  time even if the read is mapped better to some contigs than others. This makes
+  it possible to analyze each contig independent of others.
+
+* `out.hla.top`: best genotypes for HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes.
+
+* `out.hla.all`: other possible genotypes on the six HLA genes.
+
+* `out.log.*`: bwa-mem, samblaster and HLA typing log files.
+
+Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
+scripts in the package are available in the [bwa/bwakit][kit] directory.
+Packaging is done manually for now.
+
+## Limitations
+
+* HLA typing only works for high-coverage human data. The typing accuracy can
+  still be improved. We encourage researchers to develop better HLA typing tools
+  based on the intermediate output of bwakit (for each HLA gene included in the
+  index, bwakit writes all reads matching it in a separate file).
+
+* Duplicate marking only works when all reads from a single paired-end library
+  are provided as the input. This limitation is the necessary tradeoff of fast
+  MarkDuplicate provided by samblaster.
+
+* The adapter trimmer is chosen as it is fast, pipe friendly and does not
+  discard reads. However, it is conservative and suboptimal. If this is a
+  concern, it is recommended to preprocess input reads with a more sophisticated
+  adapter trimmer. We also hope existing trimmers can be modified to operate on
+  an interleaved FASTQ stream. We will replace trimadap once a better trimmer
+  meets our needs.
+
+* Bwakit can be memory demanding depends on the functionality invoked. For 30X
+  human data, bwa-mem takes about 11GB RAM with 32 threads, samblaster uses
+  close to 10GB and BAM shuffling (if the input is sorted BAM) uses several GB.
+  In the current setting, sorting uses about 10GB.
+
+
+## Package Contents  
+```
+bwa.kit
+|-- README.md                  This README file.
+|-- run-bwamem                 *Entry script* for the entire mapping pipeline.
+|-- bwa                        *BWA binary*
+|-- k8                         Interpretor for *.js scripts.
+|-- bwa-postalt.js             Post-process alignments to ALT contigs/decoys/HLA genes.
+|-- htsbox                     Used by run-bwamem for shuffling BAMs and BAM=>FASTQ.
+|-- samblaster                 MarkDuplicates for reads from the same library. v0.1.20
+|-- samtools                   SAMtools for sorting and SAM=>BAM conversion. v1.1
+|-- seqtk                      For FASTQ manipulation.
+|-- trimadap                   Trim Illumina PE sequencing adapters.
+|
+|-- run-gen-ref                *Entry script* for generating human reference genomes.
+|-- resource-GRCh38            Resources for generating GRCh38
+|   |-- hs38DH-extra.fa        Decoy and HLA gene sequences. Used by run-gen-ref.
+|   `-- hs38DH.fa.alt          ALT-to-GRCh38 alignment. Used by run-gen-ref.
+|
+|-- run-HLA                    HLA typing for sequences extracted by bwa-postalt.js.
+|-- typeHLA.sh                 Type one HLA-gene. Called by run-HLA.
+|-- typeHLA.js                 HLA typing from exon-to-contig alignment. Used by typeHLA.sh.
+|-- typeHLA-selctg.js          Select contigs overlapping HLA exons. Used by typeHLA.sh.
+|-- fermi2.pl                  Fermi2 wrapper. Used by typeHLA.sh for de novo assembly.
+|-- fermi2                     Fermi2 binary. Used by fermi2.pl.
+|-- ropebwt2                   RopeBWT2 binary. Used by fermi2.pl.
+|-- resource-human-HLA         Resources for HLA typing
+|   |-- HLA-ALT-exons.bed      Exonic regions of HLA ALT contigs. Used by typeHLA.sh.
+|   |-- HLA-CDS.fa             CDS of HLA-{A,B,C,DQA1,DQB1,DRB1} genes from IMGT/HLA-3.18.0.
+|   |-- HLA-ALT-type.txt       HLA types for each HLA ALT contig. Not used.
+|   `-- HLA-ALT-idx            BWA indices of each HLA ALT contig. Used by typeHLA.sh
+|       `-- (...)
+|
+`-- doc                        BWA documentations
+    |-- bwa.1                  Manpage
+    |-- NEWS.md                Release Notes
+    |-- README.md              GitHub README page
+    `-- README-alt.md          Documentation for ALT mapping
+```
+
+[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit
+[sb]: https://github.com/GregoryFaust/samblaster
+[ta]: https://github.com/lh3/seqtk/blob/master/trimadap.c
+[smtl]: http://www.htslib.org
+[kit]: https://github.com/lh3/bwa/tree/master/bwakit

bwakit/bwa-postalt.js

@@ -0,0 +1,524 @@
+/*****************************************************************
+ * The K8 Javascript interpreter is required to run this script. *
+ *                                                               *
+ *   Source code: https://github.com/attractivechaos/k8          *
+ *   Binary: http://sourceforge.net/projects/lh3/files/k8/       *
+ *                                                               *
+ * Data file used for generating GRCh38 ALT alignments:          *
+ *                                                               *
+ *   http://sourceforge.net/projects/bio-bwa/files/              *
+ *****************************************************************/
+
+/******************
+ *** From k8.js ***
+ ******************/
+
+// Parse command-line options. A BSD getopt() clone in javascript.
+var getopt = function(args, ostr) {
+	var oli; // option letter list index
+	if (typeof(getopt.place) == 'undefined')
+		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
+	if (getopt.place == -1) { // update scanning pointer
+		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
+			getopt.place = -1;
+			return null;
+		}
+		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
+			++getopt.ind;
+			getopt.place = -1;
+			return null;
+		}
+	}
+	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
+	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
+		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
+		if (getopt.place < 0) ++getopt.ind;
+		return '?';
+	}
+	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
+		getopt.arg = null;
+		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
+	} else { // need an argument
+		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
+			getopt.arg = args[getopt.ind].substr(getopt.place);
+		else if (args.length <= ++getopt.ind) { // no arg
+			getopt.place = -1;
+			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
+			return '?';
+		} else getopt.arg = args[getopt.ind]; // white space
+		getopt.place = -1;
+		++getopt.ind;
+	}
+	return optopt;
+}
+
+// reverse a string
+Bytes.prototype.reverse = function()
+{
+	for (var i = 0; i < this.length>>1; ++i) {
+		var tmp = this[i];
+		this[i] = this[this.length - i - 1];
+		this[this.length - i - 1] = tmp;
+	}
+}
+
+// reverse complement a DNA string
+Bytes.prototype.revcomp = function()
+{
+	if (Bytes.rctab == null) {
+		var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
+		var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
+		Bytes.rctab = [];
+		for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
+		for (var i = 0; i < s1.length; ++i)
+			Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
+	}
+	for (var i = 0; i < this.length>>1; ++i) {
+		var tmp = this[this.length - i - 1];
+		this[this.length - i - 1] = Bytes.rctab[this[i]];
+		this[i] = Bytes.rctab[tmp];
+	}
+	if (this.length&1)
+		this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
+}
+
+// create index for a list of intervals for fast interval queries; ported from bedidx.c in samtools
+function intv_ovlp(intv, bits)
+{
+	if (typeof bits == "undefined") bits = 13;
+	intv.sort(function(a,b) {return a[0]-b[0];});
+	// create the index
+	var idx = [], max = 0;
+	for (var i = 0; i < intv.length; ++i) {
+		var b = intv[i][0]>>bits;
+		var e = (intv[i][1]-1)>>bits;
+		if (b != e) {
+			for (var j = b; j <= e; ++j)
+				if (idx[j] == null) idx[j] = i;
+		} else if (idx[b] == null) idx[b] = i;
+		max = max > e? max : e;
+	}
+	// closure
+	return function(_b, _e) {
+		var x = _b >> bits;
+		if (x > max) return [];
+		var off = idx[x];
+		if (off == null) {
+			var i;
+			for (i = ((_e - 1) >> bits) - 1; i >= 0; --i)
+				if (idx[i] != null) break;
+			off = i < 0? 0 : idx[i];
+		}
+		var ovlp = [];
+		for (var i = off; i < intv.length && intv[i][0] < _e; ++i)
+			if (intv[i][1] > _b) ovlp.push(intv[i]);
+		return ovlp;
+	}
+}
+
+var re_cigar = /(\d+)([MIDSHN])/g;
+
+/******************************
+ *** Generate ALT alignment ***
+ ******************************/
+
+// given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
+function cigar2pos(cigar, pos)
+{
+	var x = 0, y = 0;
+	for (var i = 0; i < cigar.length; ++i) {
+		var op = cigar[i][0], len = cigar[i][1];
+		if (op == 'M') {
+			if (y <= pos && pos < y + len)
+				return x + (pos - y);
+			x += len, y += len;
+		} else if (op == 'D') {
+			x += len;
+		} else if (op == 'I') {
+			if (y <= pos && pos < y + len)
+				return x;
+			y += len;
+		} else if (op == 'S' || op == 'H') {
+			if (y <= pos && pos < y + len)
+				return -1;
+			y += len;
+		}
+	}
+	return -1;
+}
+
+// Parse a hit. $s is an array that looks something like ["chr1", "+12345", "100M", 5]
+// Return an object keeping various information about the alignment.
+function parse_hit(s, opt)
+{
+	var h = {};
+	h.ctg = s[0];
+	h.start = parseInt(s[1].substr(1)) - 1;
+	h.rev = (s[1].charAt(0) == '-');
+	h.cigar = s[2];
+	h.NM = parseInt(s[3]);
+	h.hard = false;
+	var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip;
+	l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
+	while ((m = re_cigar.exec(h.cigar)) != null) {
+		var l = parseInt(m[1]);
+		if (m[2] == 'M') l_match += l;
+		else if (m[2] == 'D') ++n_del, l_del += l;
+		else if (m[2] == 'I') ++n_ins, l_ins += l;
+		else if (m[2] == 'N') l_skip += l;
+		else if (m[2] == 'H' || m[2] == 'S') {
+			l_clip += l;
+			if (m[2] == 'H') h.hard = true;
+		}
+	}
+	h.end = h.start + l_match + l_del + l_skip;
+	h.NM = h.NM > l_del + l_ins? h.NM : l_del + l_ins;
+	h.score = Math.floor((opt.a * l_match - (opt.a + opt.b) * (h.NM - l_del - l_ins) - opt.o * (n_del + n_ins) - opt.e * (l_del + l_ins)) / opt.a + .499);
+	h.l_query = l_match + l_ins + l_clip;
+	return h;
+}
+
+function print_buffer(buf2, fp_hla, hla) // output alignments
+{
+	if (buf2.length == 0) return;
+	for (var i = 0; i < buf2.length; ++i)
+		print(buf2[i].join("\t"));
+	if (fp_hla != null) {
+		var name = buf2[0][0] + '/' + (buf2[0][1]>>6&3) + ((buf2[0][1]&16)? '-' : '+');
+		for (var x in hla) {
+			if (fp_hla[x] != null);
+				fp_hla[x].write('@' + name + '\n' + buf2[0][9] + '\n+\n' + buf2[0][10] + '\n');
+		}
+	}
+}
+
+function collect_hla_hits(idx, ctg, start, end, hla) // collect reads hit to HLA genes
+{
+	var m, ofunc = idx[ctg];
+	if (ofunc == null) return;
+	var ovlp_alt = ofunc(start, end);
+	for (var i = 0; i < ovlp_alt.length; ++i)
+		if ((m = /^(HLA-[^\s\*]+)\*\d+/.exec(ovlp_alt[i][2])) != null)
+			hla[m[1]] = true;
+}
+
+function bwa_postalt(args)
+{
+	var version = "r985";
+	var c, opt = { a:1, b:4, o:6, e:1, min_mapq:10, min_sc:90, max_nm_sc:10, min_pa_ratio:1 };
+
+	while ((c = getopt(args, 'vp:r:')) != null) {
+		if (c == 'p') opt.pre = getopt.arg;
+		else if (c == 'r') opt.min_pa_ratio = parseFloat(getopt.arg);
+		else if (c == 'v') { print(version); exit(0); }
+	}
+	if (opt.min_pa_ratio > 1.) opt.min_pa_ratio = 1.;
+
+	if (args.length == getopt.ind) {
+		print("");
+		print("Usage:   k8 bwa-postalt.js [options] <alt.sam> [aln.sam]\n");
+		print("Options: -p STR     prefix of output files containting sequences matching HLA genes [null]");
+		print("         -r FLOAT   reduce mapQ to 0 if not overlapping lifted best and pa<FLOAT ["+opt.min_pa_ratio+"]");
+		print("         -v         show version number");
+		print("");
+		print("Note: This script extracts the XA tag, lifts the mapping positions of ALT hits to");
+		print("      the primary assembly, groups them and then estimates mapQ across groups. If");
+		print("      a non-ALT hit overlaps a lifted ALT hit, its mapping quality is set to the");
+		print("      smaller between its original mapQ and the adjusted mapQ of the ALT hit. If");
+		print("      multiple ALT hits are lifted to the same position, they will yield new SAM");
+		print("      lines with the same mapQ.");
+		print("");
+		exit(1);
+	}
+
+	var aux = new Bytes(); // used for reverse and reverse complement
+	var buf = new Bytes(); // line reading buffer
+
+	// read ALT-to-REF alignment
+	var intv_alt = {}, intv_pri = {}, hla_ctg = {}, is_alt = {}, hla_chr = null;
+	var file = new File(args[getopt.ind]);
+	while (file.readline(buf) >= 0) {
+		var line = buf.toString();
+		if (line.charAt(0) == '@') continue;
+		var t = line.split("\t");
+		if (t.length < 11) continue; // incomplete lines
+		is_alt[t[0]] = true;
+		var pos = parseInt(t[3]) - 1;
+		var flag = parseInt(t[1]);
+		if ((flag&4) || t[2] == '*') continue;
+		var m, cigar = [], l_qaln = 0, l_tlen = 0, l_qclip = 0;
+		if ((m = /^(HLA-[^\s\*]+)\*\d+/.exec(t[0])) != null) { // read HLA contigs
+			if (hla_ctg[m[1]] == null) hla_ctg[m[1]] = 0;
+			++hla_ctg[m[1]];
+			hla_chr = t[2];
+		}
+		while ((m = re_cigar.exec(t[5])) != null) {
+			var l = parseInt(m[1]);
+			cigar.push([m[2] != 'H'? m[2] : 'S', l]); // convert hard clip to soft clip
+			if (m[2] == 'M') l_qaln += l, l_tlen += l;
+			else if (m[2] == 'I') l_qaln += l;
+			else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
+			else if (m[2] == 'D' || m[2] == 'N') l_tlen += l;
+		}
+		var j = flag&16? cigar.length-1 : 0;
+		var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
+		if (intv_alt[t[0]] == null) intv_alt[t[0]] = [];
+		intv_alt[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, pos - 1, cigar, pos + l_tlen]);
+		if (intv_pri[t[2]] == null) intv_pri[t[2]] = [];
+		intv_pri[t[2]].push([pos, pos + l_tlen, t[0]]);
+	}
+	file.close();
+	var idx_alt = {}, idx_pri = {};
+	for (var ctg in intv_alt) idx_alt[ctg] = intv_ovlp(intv_alt[ctg]);
+	for (var ctg in intv_pri) idx_pri[ctg] = intv_ovlp(intv_pri[ctg]);
+
+	// initialize the list of HLA contigs
+	var fp_hla = null;
+	if (opt.pre) {
+		fp_hla = {};
+		for (var h in hla_ctg)
+			fp_hla[h] = new File(opt.pre + '.' + h + '.fq', "w");
+	}
+
+	// process SAM
+	var buf2 = [], hla = {};
+	file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
+	while (file.readline(buf) > 0) {
+		var m, line = buf.toString();
+
+		if (line.charAt(0) == '@') { // print and then skip the header line
+			print(line);
+			continue;
+		}
+
+		var t = line.split("\t");
+		t[1] = parseInt(t[1]); t[3] = parseInt(t[3]); t[4] = parseInt(t[4]);
+
+		// print bufferred reads
+		if (buf2.length && (buf2[0][0] != t[0] || (buf2[0][1]&0xc0) != (t[1]&0xc0))) {
+			print_buffer(buf2, fp_hla, hla);
+			buf2 = [], hla = {};
+		}
+
+		// skip unmapped lines
+		if (t[1]&4) {
+			buf2.push(t);
+			continue;
+		}
+
+		// parse the reported hit
+		var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
+		var flag = t[1];
+		var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
+		if (t[2] == hla_chr) collect_hla_hits(idx_pri, h.ctg, h.start, h.end, hla);
+
+		if (h.hard) { // the following does not work with hard clipped alignments
+			buf2.push(t);
+			continue;
+		}
+		var hits = [h];
+
+		// parse hits in the XA tag
+		if ((m = /\tXA:Z:(\S+)/.exec(line)) != null) {
+			var XA_strs = m[1].split(";");
+			for (var i = 0; i < XA_strs.length; ++i)
+				if (XA_strs[i] != '') // as the last symbol in an XA tag is ";", the last split is an empty string
+					hits.push(parse_hit(XA_strs[i].split(","), opt));
+		}
+
+		// check if there are ALT hits
+		var has_alt = false;
+		for (var i = 0; i < hits.length; ++i)
+			if (is_alt[hits[i].ctg] != null) {
+				has_alt = true;
+				break;
+			}
+		if (!has_alt) {
+			buf2.push(t);
+			continue;
+		}
+
+		// lift mapping positions to the primary assembly
+		var n_rpt_lifted = 0, rpt_lifted = null;
+		for (var i = 0; i < hits.length; ++i) {
+			var a, h = hits[i];
+
+			if (idx_alt[h.ctg] == null || (a = idx_alt[h.ctg](h.start, h.end)) == null || a.length == 0)
+				continue;
+
+			// find the approximate position on the primary assembly
+			var lifted = [];
+			for (var j = 0; j < a.length; ++j) {
+				var s, e;
+				if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
+					s = cigar2pos(a[j][6], h.start);
+					e = cigar2pos(a[j][6], h.end - 1) + 1;
+				} else {
+					s = cigar2pos(a[j][6], a[j][2] - h.end);
+					e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
+				}
+				if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
+				s += a[j][5]; e += a[j][5];
+				lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
+				if (i == 0) ++n_rpt_lifted;
+			}
+			if (i == 0 && n_rpt_lifted == 1) rpt_lifted = lifted[0].slice(0);
+			if (lifted.length) hits[i].lifted = lifted;
+		}
+
+		// prepare for hits grouping
+		for (var i = 0; i < hits.length; ++i) { // set keys for sorting
+			if (hits[i].lifted != null) // TODO: only the first element in lifted[] is used
+				hits[i].pctg = hits[i].lifted[0][0], hits[i].pstart = hits[i].lifted[0][2], hits[i].pend = hits[i].lifted[0][3];
+			else hits[i].pctg = hits[i].ctg, hits[i].pstart = hits[i].start, hits[i].pend = hits[i].end;
+			hits[i].i = i; // keep the original index
+		}
+
+		// group hits based on the lifted positions on non-ALT sequences
+		if (hits.length > 1) {
+			hits.sort(function(a,b) { return a.pctg != b.pctg? (a.pctg < b.pctg? -1 : 1) : a.pstart - b.pstart });
+			var last_chr = null, end = 0, g = -1;
+			for (var i = 0; i < hits.length; ++i) {
+				if (last_chr != hits[i].pctg) ++g, last_chr = hits[i].pctg, end = 0;
+				else if (hits[i].pstart >= end) ++g;
+				hits[i].g = g;
+				end = end > hits[i].pend? end : hits[i].pend;
+			}
+		} else hits[0].g = 0;
+
+		// find the index and group id of the reported hit; find the size of the reported group
+		var reported_g = null, reported_i = null, n_group0 = 0;
+		if (hits.length > 1) {
+			for (var i = 0; i < hits.length; ++i)
+				if (hits[i].i == 0)
+					reported_g = hits[i].g, reported_i = i;
+			for (var i = 0; i < hits.length; ++i)
+				if (hits[i].g == reported_g)
+					++n_group0;
+		} else {
+			if (is_alt[hits[0].ctg] == null) { // no need to go through the following if the single hit is non-ALT
+				buf2.push(t);
+				continue;
+			}
+			reported_g = reported_i = 0, n_group0 = 1;
+		}
+
+		// re-estimate mapping quality if necessary
+		var mapQ, ori_mapQ = t[4];
+		if (n_group0 > 1) {
+			var group_max = [];
+			for (var i = 0; i < hits.length; ++i) {
+				var g = hits[i].g;
+				if (group_max[g] == null || group_max[g][0] < hits[i].score)
+					group_max[g] = [hits[i].score, g];
+			}
+			if (group_max.length > 1)
+				group_max.sort(function(x,y) {return y[0]-x[0]});
+			if (group_max[0][1] == reported_g) { // the best hit is the hit reported in SAM
+				mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
+			} else mapQ = 0;
+			mapQ = mapQ < 60? mapQ : 60;
+			if (idx_alt[t[2]] == null) mapQ = mapQ < ori_mapQ? mapQ : ori_mapQ;
+			else mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
+		} else mapQ = t[4];
+
+		// find out whether the read is overlapping HLA genes
+		if (hits[reported_i].pctg == hla_chr) {
+			var rpt_start = 1<<30, rpt_end = 0;
+			for (var i = 0; i < hits.length; ++i) {
+				var h = hits[i];
+				if (h.g == reported_g) {
+					rpt_start = rpt_start < h.pstart? rpt_start : h.pstart;
+					rpt_end   = rpt_end   > h.pend  ? rpt_end   : h.pend;
+				}
+			}
+			collect_hla_hits(idx_pri, hla_chr, rpt_start, rpt_end, hla);
+		}
+
+		// adjust the mapQ of the primary hits
+		if (n_rpt_lifted <= 1) {
+			var l = n_rpt_lifted == 1? rpt_lifted : null;
+			for (var i = 0; i < buf2.length; ++i) {
+				var s = buf2[i], is_ovlp = true;
+				if (l != null) {
+					if (l[0] != s[2]) is_ovlp = false; // different chr
+					else if (((s[1]&16) != 0) != l[1]) is_ovlp = false; // different strand
+					else {
+						var start = s[3] - 1, end = start;
+						while ((m = re_cigar.exec(t[5])) != null)
+							if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
+								end += parseInt(m[1]);
+						if (!(start < l[3] && l[2] < end)) is_ovlp = false; // no overlap
+					}
+				} else is_ovlp = false;
+				// get the "pa" tag if present
+				var om = -1, pa = 10.;
+				for (var j = 11; j < s.length; ++j)
+					if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
+						om = parseInt(m[1]);
+					else if ((m = /^pa:f:(\S+)/.exec(s[j])) != null)
+						pa = parseFloat(m[1]);
+				if (is_ovlp) { // overlapping the lifted hit
+					if (om > 0) s[4] = om;
+					s[4] = s[4] < mapQ? s[4] : mapQ;
+				} else if (pa < opt.min_pa_ratio) { // not overlapping; has a small pa
+					if (om < 0) s.push("om:i:" + s[4]);
+					s[4] = 0;
+				}
+			}
+		}
+
+		// generate lifted_str
+		for (var i = 0; i < hits.length; ++i) {
+			if (hits[i].lifted && hits[i].lifted.length) {
+				var u = '', lifted = hits[i].lifted;
+				for (var j = 0; j < lifted.length; ++j)
+					u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
+				hits[i].lifted_str = u;
+			}
+		}
+
+		// stage the reported hit
+		t[4] = mapQ;
+		if (n_group0 > 1) t.push("om:i:"+ori_mapQ);
+		if (hits[reported_i].lifted_str) t.push("lt:Z:" + hits[reported_i].lifted_str);
+		buf2.push(t);
+
+		// stage the hits generated from the XA tag
+		var cnt = 0, rs = null, rq = null; // rq: reverse quality; rs: reverse complement sequence
+		var rg = (m = /\t(RG:Z:\S+)/.exec(line)) != null? m[1] : null;
+		for (var i = 0; i < hits.length; ++i) {
+			if (hits[i].g != reported_g || i == reported_i) continue;
+			if (idx_alt[hits[i].ctg] == null) continue;
+			var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]];
+			if (t[6] == '=' && s[2] != t[2]) s[6] = t[2];
+			// print sequence/quality and set the rev flag
+			if (hits[i].rev == hits[reported_i].rev) {
+				s.push(t[9], t[10]);
+				s[1] = flag | 0x800;
+			} else { // we need to write the reverse sequence
+				if (rs == null || rq == null) {
+					aux.length = 0;
+					aux.set(t[9], 0); aux.revcomp(); rs = aux.toString();
+					aux.set(t[10],0); aux.reverse(); rq = aux.toString();
+				}
+				s.push(rs, rq);
+				s[1] = (flag ^ 0x10) | 0x800;
+			}
+			s.push("NM:i:" + hits[i].NM);
+			if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
+			if (rg != null) s.push(rg);
+			buf2.push(s);
+		}
+	}
+	print_buffer(buf2, fp_hla, hla);
+	file.close();
+	if (fp_hla != null)
+		for (var h in fp_hla)
+			fp_hla[h].close();
+
+	buf.destroy();
+	aux.destroy();
+}
+
+bwa_postalt(arguments);

bwakit/run-HLA

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+ctg_opt=""
+if [ $# -gt 1 ] && [ $1 == '-A' ]; then
+	ctg_opt="-A"
+	shift
+fi
+
+if [ $# -eq 0 ]; then
+	echo "Usage: $0 <prefix>"
+	exit 1
+fi
+
+for f in $1.HLA-*.fq; do
+	gene=`echo $f | perl -pe 's/^.*(HLA-[A-Z]+[0-9]*).*fq$/$1/'`
+	echo -e "\n*** Processing gene $gene...\n" >&2
+	`dirname $0`/typeHLA.sh $ctg_opt $1 $gene
+done
+
+ls $1.HLA-*.gt | xargs -i echo grep ^GT {} \| head -1 | sh | sed "s,^GT,$1,"

bwakit/run-bwamem

@@ -0,0 +1,187 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opts = (t=>1);
+getopts("MPSadskHo:R:x:t:", \%opts);
+
+die('
+Usage:   run-bwamem [options] <idxbase> <file1> [file2]
+
+Options: -o STR    prefix for output files                       [inferred from input]
+         -R STR    read group header line such as \'@RG\tID:foo\tSM:bar\'         [null]
+         -x STR    read type: pacbio, ont2d or intractg                      [default]
+                   intractg: intra-species contig (kb query, highly similar)
+                   pacbio:   pacbio subreads (~10kb query, high error rate)
+                   ont2d:    Oxford Nanopore reads (~10kb query, higher error rate)
+         -t INT    number of threads                                               [1]
+
+         -H        apply HLA typing
+         -a        trim HiSeq2000/2500 PE resequencing adapters (via trimadap)
+         -d        mark duplicate (via samblaster)
+         -S        for BAM input, don\'t shuffle
+         -s        sort the output alignment (via samtools; requring more RAM)
+         -k        keep temporary files generated by typeHLA
+         -M        mark shorter split hits as secondary
+
+Examples:
+
+ * Map paired-end reads to GRCh38+ALT+decoy+HLA and perform HLA typing:
+
+     run-bwamem -o prefix -t8 -HR"@RG\tID:foo\tSM:bar" hs38DH.fa read1.fq.gz read2.fq.gz
+
+   Note: HLA typing is only effective for high-coverage data. The typing accuracy varies
+   with the quality of input. It is only intended for research purpose, not for diagnostic.
+
+ * Remap coordinate-sorted BAM, transfer read groups tags, trim Illumina PE adapters and
+   sort the output. The BAM may contain single-end or paired-end reads, or a mixture of
+   the two types. Specifying -R stops read group transfer.
+
+     run-bwamem -sao prefix hs38DH.fa old-srt.bam
+
+   Note: the adaptor trimmer included in bwa.kit is chosen because it fits the current
+   mapping pipeline better. It is conservative and suboptimal. A more sophisticated
+   trimmer is recommended if this becomes a concern.
+
+ * Remap name-grouped BAM and mark duplicates:
+ 
+     run-bwamem -Sdo prefix hs38DH.fa old-unsrt.bam
+
+   Note: streamed duplicate marking requires all reads from a single paired-end library
+   to be aligned at the same time.
+
+Output files:
+
+  {-o}.aln.bam - final alignment
+  {-o}.hla.top - best genotypes for the 6 classical HLA genes (if there are HLA-* contigs)
+  {-o}.hla.all - additional HLA genotypes consistent with data
+  {-o}.log.*   - log files
+
+') if @ARGV < 2;
+
+my $idx = $ARGV[0];
+
+my $exepath = $0 =~/^\S+\/[^\/\s]+/? $0 : &which($0);
+my $root = $0 =~/^(\S+)\/[^\/\s]+/? $1 : undef;
+$root = $exepath =~/^(\S+)\/[^\/\s]+/? $1 : undef if !defined($root);
+die "ERROR: failed to locate the 'bwa.kit' directory\n" if !defined($root);
+
+die("ERROR: failed to locate the BWA index. Please run '$root/bwa index -p $idx ref.fa'.\n")
+  unless (-f "$idx.bwt" && -f "$idx.pac" && -f "$idx.sa" && -f "$idx.ann" && -f "$idx.amb");
+
+if (@ARGV >= 3 && $ARGV[1] =~ /\.(bam|sam|sam\.gz)$/) {
+	warn("WARNING: for SAM/BAM input, only the first sequence file is used.\n");
+	@ARGV = 2;
+}
+
+if (defined($opts{p}) && @ARGV >= 3) {
+	warn("WARNING: option -P is ignored as there are two input sequence files.\n");
+	delete $opts{p};
+}
+
+my $prefix;
+if (defined $opts{o}) {
+	$prefix = $opts{o};
+} elsif (@ARGV >= 3) {
+	my $len = length($ARGV[1]) < length($ARGV[2])? length($ARGV[1]) : length($ARGV[2]);
+	my $i;
+	for ($i = 0; $i < $len; ++$i) {
+		last if substr($ARGV[1], $i, 1) ne substr($ARGV[2], $i, 1)
+	}
+	$prefix = substr($ARGV[1], 0, $i) if $i > 0;
+} elsif ($ARGV[1] =~ /^(\S+)\.(fastq|fq|fasta|fa|mag|mag\.gz|fasta\.gz|fa\.gz|fastq\.gz|fq\.gz|bam)$/) {
+	$prefix = $1;
+}
+die("ERROR: failed to identify the prefix for output. Please specify -o.\n") unless defined($prefix);
+
+my $size = 0;
+my $comp_ratio = 3.;
+for my $f (@ARGV[1..$#ARGV]) {
+	my @a = stat($f);
+	my $s = $a[7];
+	die("ERROR: failed to read file $f\n") if !defined($s);
+	$s *= $comp_ratio if $f =~ /\.(gz|bam)$/;
+	$size += int($s) + 1;
+}
+
+my $is_pe = (defined($opts{p}) || @ARGV >= 3)? 1 : 0;
+my $is_bam = $ARGV[1] =~ /\.bam$/? 1 : 0;
+
+if (defined($opts{x})) {
+	delete($opts{d}); delete($opts{a}); delete $opts{p};
+}
+
+# for BAM input, find @RG header lines
+my @RG_lines = ();
+if ($is_bam && !defined($opts{R})) {
+	my $fh;
+	open($fh, "$root/samtools view -H $ARGV[1] |") || die;
+	while (<$fh>) {
+		chomp;
+		if (/^\@RG\t/) {
+			s/\t/\\t/g;
+			push(@RG_lines, "-H'$_'");
+		}
+	}
+	close($fh);
+}
+
+warn("WARNING: many programs require read groups. Please specify with -R if you can.\n") if !defined($opts{R}) && @RG_lines == 0;
+
+my $cmd = '';
+if ($is_bam) {
+	my $cmd_sam2bam = "cat $ARGV[1] \\\n";
+	my $ntmps = int($size / 4e9) + 1;
+	my $cmd_shuf = !defined($opts{S})? "  | $root/htsbox bamshuf -uOn$ntmps - $prefix.shuf \\\n" : "";
+	my $bam2fq_opt = @RG_lines > 0? " -t" : "";
+	my $cmd_bam2fq = "  | $root/htsbox bam2fq -O$bam2fq_opt - \\\n";
+	$cmd = $cmd_sam2bam . $cmd_shuf . $cmd_bam2fq;
+} elsif (@ARGV >= 3) {
+	$cmd = "$root/seqtk mergepe $ARGV[1] $ARGV[2] \\\n";
+} else {
+	$cmd = "cat $ARGV[1] \\\n";
+}
+
+my $bwa_opts = "-p " . ($opts{t} > 1? "-t$opts{t} " : "") . (defined($opts{x})? "-x $opts{x} " : "") . (defined($opts{R})? "-R'$opts{R}' " : "") . (defined($opts{M})? "-M " : "");
+$bwa_opts .= join(" ", @RG_lines) . " -C " if @RG_lines > 0;
+
+$cmd .= "  | $root/trimadap 2> $prefix.log.trim \\\n" if defined($opts{a});
+$cmd .= "  | $root/bwa mem $bwa_opts$ARGV[0] - 2> $prefix.log.bwamem \\\n";
+$cmd .= "  | $root/samblaster 2> $prefix.log.dedup \\\n" if defined($opts{d});
+
+my $has_hla = 0;
+if (-f "$ARGV[0].alt" && !defined($opts{P})) {
+	my $fh;
+	open($fh, "$ARGV[0].alt") || die;
+	while (<$fh>) {
+		$has_hla = 1 if /^HLA-[^\s\*]+\*\d+/;
+	}
+	close($fh);
+	my $hla_pre = $has_hla? "-p $prefix.hla " : "";
+	$cmd .= "  | $root/k8 $root/bwa-postalt.js $hla_pre$ARGV[0].alt \\\n";
+}
+
+my $t_sort = $opts{t} < 4? $opts{t} : 4;
+$cmd .= defined($opts{s})? "  | $root/samtools sort -@ $t_sort -m1G - -o $prefix.aln.bam;\n" : "  | $root/samtools view -1 - > $prefix.aln.bam;\n";
+
+if ($has_hla && defined($opts{H}) && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
+	$cmd .= "$root/run-HLA ". (defined($opts{x}) && $opts{x} eq 'intractg'? "-A " : "") . "$prefix.hla > $prefix.hla.top 2> $prefix.log.hla;\n";
+	$cmd .= "touch $prefix.hla.HLA-dummy.gt; cat $prefix.hla.HLA*.gt | grep ^GT | cut -f2- > $prefix.hla.all;\n";
+	$cmd .= "rm -f $prefix.hla.HLA*;\n" unless defined($opts{k});
+}
+
+print $cmd;
+
+sub which
+{
+	my $file = shift;
+	my $path = (@_)? shift : $ENV{PATH};
+	return if (!defined($path));
+	foreach my $x (split(":", $path)) {
+		$x =~ s/\/$//;
+		return "$x/$file" if (-x "$x/$file");
+	}
+	return;
+}

bwakit/run-gen-ref

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+root=`dirname $0`
+
+url38="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz"
+url37d5="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
+
+if [ $# -eq 0 ]; then
+	echo "Usage: $0 <hs38|hs38a|hs38DH|hs37|hs37d5>"
+	echo "Analysis sets:"
+	echo "  hs38     primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV"
+	echo "  hs38a    hs38 plus ALT contigs"
+	echo "  hs38DH   hs38a plus decoy contigs and HLA genes (recommended for GRCh38 mapping)"
+	echo "  hs37     primary assembly of GRCh37 (used by 1000g phase 1) plus the EBV genome"
+	echo "  hs37d5   hs37 plus decoy contigs (used by 1000g phase 3)"
+	echo ""
+	echo "Note: This script downloads human reference genomes. For hs38a and hs38DH, it needs additional"
+	echo "      sequences and ALT-to-REF mapping included in the bwa.kit package."
+	exit 1;
+fi
+
+if [ $1 == "hs38DH" ]; then
+	(wget -O- $url38 | gzip -dc; cat $root/resource-GRCh38/hs38DH-extra.fa) > $1.fa
+	[ ! -f $1.fa.alt ] && cp $root/resource-GRCh38/hs38DH.fa.alt $1.fa.alt
+elif [ $1 == "hs38a" ]; then
+	wget -O- $url38 | gzip -dc > $1.fa
+	[ ! -f $1.fa.alt ] && grep _alt $root/resource-GRCh38/hs38DH.fa.alt > $1.fa.alt
+elif [ $1 == "hs38" ]; then
+	wget -O- $url38 | gzip -dc | awk '/^>/{f=/_alt/?0:1}f' > $1.fa
+elif [ $1 == "hs37d5" ]; then
+	wget -O- $url37d5 | gzip -dc > $1.fa 2>/dev/null
+elif [ $1 == "hs37" ]; then
+	wget -O- $url37d5 | gzip -dc 2>/dev/null | awk '/^>/{f=/>hs37d5/?0:1}f' > $1.fa
+else
+	echo "ERROR: unknown genome build"
+fi
+
+[ ! -f $1.fa.bwt ] && echo -e "\nPlease run 'bwa index $1.fa'...\n"
+

bwakit/typeHLA-selctg.js

@@ -0,0 +1,62 @@
+var min_ovlp = 30;
+
+if (arguments.length < 3) {
+	print("Usage: k8 selctg.js <HLA-gene> <HLA-ALT-exons.bed> <ctg-to-ALT.sam> [min_ovlp="+min_ovlp+"]");
+	exit(1);
+}
+
+if (arguments.length >= 4) min_ovlp = parseInt(arguments[3]);
+var gene = arguments[0];
+
+var buf = new Bytes();
+
+var h = {};
+var file = new File(arguments[1]);
+while (file.readline(buf) >= 0) {
+	var t = buf.toString().split("\t");
+	if (t[3] != gene) continue;
+	if (h[t[0]] == null) h[t[0]] = [];
+	h[t[0]].push([parseInt(t[1]), parseInt(t[2])]);
+}
+file.close();
+
+var s = {}, re = /(\d+)([MIDSHN])/g;
+file = new File(arguments[2]);
+while (file.readline(buf) >= 0) {
+	var line = buf.toString();
+	var m, t = line.split("\t");
+	var x = h[t[2]];
+	if (x == null) continue;
+
+	var start = parseInt(t[3]) - 1, end = start;
+	while ((m = re.exec(t[5])) != null) // parse CIGAR to get the end position
+		if (m[2] == 'M' || m[2] == 'D')
+			end += parseInt(m[1]);
+
+	var max_ovlp = 0;
+	for (var i = 0; i < x.length; ++i) {
+		var max_left = x[i][0] > start? x[i][0] : start;
+		var min_rght = x[i][1] < end  ? x[i][1] : end;
+		max_ovlp = max_ovlp > min_rght - max_left? max_ovlp : min_rght - max_left;
+	}
+
+	var AS = null, XS = null;
+	if ((m = /AS:i:(\d+)/.exec(line)) != null) AS = parseInt(m[1]);
+	if ((m = /XS:i:(\d+)/.exec(line)) != null) XS = parseInt(m[1]);
+
+	if (s[t[0]] == null) s[t[0]] = [];
+	s[t[0]].push([AS, XS, max_ovlp]);
+}
+file.close();
+
+buf.destroy();
+
+for (var x in s) {
+	var is_rejected = false, y = s[x];
+	y.sort(function(a,b) {return b[0]-a[0]});
+	for (var i = 0; i < y.length && y[i][0] == y[0][0]; ++i)
+		if (y[0][2] < min_ovlp || y[i][0] == y[i][1])
+			is_rejected = true;
+	if (is_rejected) continue;
+	print(x);
+}

bwakit/typeHLA.js

@@ -0,0 +1,496 @@
+/*****************************************************************
+ * The K8 Javascript interpreter is required to run this script. *
+ *                                                               *
+ *   Source code: https://github.com/attractivechaos/k8          *
+ *   Binary: http://sourceforge.net/projects/lh3/files/k8/       *
+ *****************************************************************/
+
+var getopt = function(args, ostr) {
+	var oli; // option letter list index
+	if (typeof(getopt.place) == 'undefined')
+		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
+	if (getopt.place == -1) { // update scanning pointer
+		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
+			getopt.place = -1;
+			return null;
+		}
+		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
+			++getopt.ind;
+			getopt.place = -1;
+			return null;
+		}
+	}
+	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
+	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
+		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
+		if (getopt.place < 0) ++getopt.ind;
+		return '?';
+	}
+	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
+		getopt.arg = null;
+		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
+	} else { // need an argument
+		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
+			getopt.arg = args[getopt.ind].substr(getopt.place);
+		else if (args.length <= ++getopt.ind) { // no arg
+			getopt.place = -1;
+			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
+			return '?';
+		} else getopt.arg = args[getopt.ind]; // white space
+		getopt.place = -1;
+		++getopt.ind;
+	}
+	return optopt;
+}
+
+/************************
+ * Command line parsing *
+ ************************/
+
+var ver = "r19";
+var c, thres_len = 50, thres_ratio = .8, thres_nm = 5, thres_frac = .33, dbg = false;
+
+// parse command line options
+while ((c = getopt(arguments, "vdl:n:f:")) != null) {
+	if (c == 'l') thres_len = parseInt(getopt.arg);
+	else if (c == 'n') thres_nm = parseInt(getopt.arg);
+	else if (c == 'd') dbg = true;
+	else if (c == 'f') thres_frac = parseFloat(getopt.arg);
+	else if (c == 'v') { print(ver); exit(0); }
+}
+if (arguments.length == getopt.ind) {
+	print("");
+	print("Usage:   k8 typeHLA.js [options] <exon-to-contig.sam>\n");
+	print("Options: -n INT     drop a contig if the edit distance to the closest gene is >INT ["+thres_nm+"]");
+	print("         -l INT     drop a contig if its match too short ["+thres_len+"]");
+	print("         -f FLOAT   drop inconsistent contigs if their length <FLOAT fraction of total length ["+thres_ratio.toFixed(2)+"]");
+	print("         -d         output extra info for debugging");
+	print("         -v         show version number");
+	print("");
+	print("Note: The output is TAB delimited with each GT line consisting of allele1, allele2,");
+	print("      #mismatches/gaps on primary exons, #mismatches/gaps on other exons and #exons");
+	print("      used in typing. If unusure, use the first GT line as the final genotype.\n");
+	exit(1);
+}
+
+/*********************************
+ * Read gene-to-contig alignment *
+ *********************************/
+
+var file = new File(arguments[getopt.ind]);
+var buf = new Bytes();
+var re_cigar = /(\d+)([MIDSH])/g;
+
+var len = {}, list = [], gcnt = [];
+while (file.readline(buf) >= 0) {
+	var m, mm, line = buf.toString();
+	var t = line.split("\t");
+	var flag = parseInt(t[1]);
+	// SAM header
+	if (t[0].charAt(0) == '@') {
+		if (t[0] == '@SQ' && (m = /LN:(\d+)/.exec(line)) != null && (mm = /SN:(\S+)/.exec(line)) != null)
+			len[mm[1]] = parseInt(m[1]);
+		continue;
+	}
+	// parse gene name and exon number
+	var gene = null, exon = null;
+	if ((m = /^(HLA-[^\s_]+)_(\d+)/.exec(t[0])) != null) {
+		gene = m[1], exon = parseInt(m[2]) - 1;
+		if (gcnt[exon] == null) gcnt[exon] = {};
+		gcnt[exon][gene] = true;
+	}
+	if (gene == null || exon == null || t[2] == '*') continue;
+	// parse clipping and aligned length
+	var x = 0, ts = parseInt(t[3]) - 1, te = ts, clip = [0, 0];
+	while ((m = re_cigar.exec(t[5])) != null) {
+		var l = parseInt(m[1]);
+		if (m[2] == 'M') x += l, te += l;
+		else if (m[2] == 'I') x += l;
+		else if (m[2] == 'D') te += l;
+		else if (m[2] == 'S' || m[2] == 'H') clip[x==0?0:1] = l;
+	}
+	var tl = len[t[2]];
+	var left  = ts < clip[0]? ts : clip[0];
+	var right = tl - te < clip[1]? tl - te : clip[1];
+	var qs, qe, ql = clip[0] + x + clip[1];
+	if (flag & 16) qs = clip[1], qe = ql - clip[0];
+	else qs = clip[0], qe = ql - clip[1];
+	var nm = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
+	list.push([t[2], gene, exon, ts, te, nm, left + right, qs, qe, ql]); // left+right should be 0 given a prefix-suffix alignment
+}
+
+buf.destroy();
+file.close();
+
+/**************************************
+ * Prepare data structures for typing *
+ **************************************/
+
+// identify the primary exons, the exons associated with most genes
+var pri_exon = [], n_pri_exons;
+{
+	var cnt = [], max = 0;
+	// count the number of genes per exon and track the max
+	for (var e = 0; e < gcnt.length; ++e) {
+		if (gcnt[e] != null) {
+			var c = 0, h = gcnt[e];
+			for (var x in h) ++c;
+			cnt[e] = c;
+			max = max > c? max : c;
+		} else cnt[e] = 0;
+	}
+	warn("- Number of genes for each exon: [" +cnt.join(",") + "]");
+	// find primary exons
+	var pri_list = [];
+	for (var e = 0; e < cnt.length; ++e) {
+		if (cnt[e] == max) pri_list.push(e + 1);
+		pri_exon[e] = cnt[e] == max? 1 : 0;
+	}
+	warn("- List of primary exon(s): ["+pri_list.join(",")+"]");
+	n_pri_exons = pri_list.length;
+}
+
+// convert strings to integers (for performance)
+var ghash = {}, glist = [], chash = {}, clist = [], elist = [];
+for (var i = 0; i < list.length; ++i) {
+	if (ghash[list[i][1]] == null) {
+		ghash[list[i][1]] = glist.length;
+		glist.push(list[i][1]);
+	}
+	if (chash[list[i][0]] == null) {
+		chash[list[i][0]] = clist.length;
+		clist.push(list[i][0]);
+	}
+	var g = ghash[list[i][1]];
+	if (elist[g] == null) elist[g] = {};
+	elist[g][list[i][2]] = true;
+}
+
+// extract the 3rd and 4th digits
+var gsub = [], gsuf = [];
+for (var i = 0; i < glist.length; ++i) {
+	var m = /^HLA-[^*\s]+\*\d+:(\d+).*([A-Z]?)$/.exec(glist[i]);
+	gsub[i] = parseInt(m[1]);
+	gsuf[i] = /[A-Z]$/.test(glist[i])? 1 : 0;
+}
+
+/*************************************************
+ * Collect genes with perfect matches on primary *
+ *************************************************/
+
+// collect exons with fully covered by perfect match(es)
+var perf_exons = [];
+
+function push_perf_exons(matches, last)
+{
+	matches.sort(function(a, b) { return a[0]-b[0]; });
+	var cov = 0, start = 0, end = 0;
+	for (var i = 0; i < matches.length; ++i) {
+		if (matches[i][3] > 0) continue;
+		if (matches[i][0] <= end)
+			end = end > matches[i][1]? end : matches[i][1];
+		else cov += end - start, start = matches[i][0], end = matches[i][1];
+	}
+	cov += end - start;
+	if (matches[0][2] == cov) {
+		if (perf_exons[last[1]] == null) perf_exons[last[1]] = [];
+		//print(last[0], last[1], ghash[last[0]]);
+		perf_exons[last[1]].push(ghash[last[0]]);
+	}
+}
+
+var last = [null, -1], matches = [];
+for (var i = 0; i < list.length; ++i) {
+	var li = list[i];
+	if (last[0] != li[1] || last[1] != li[2]) {
+		if (matches.length) push_perf_exons(matches, last);
+		matches = [];
+		last = [li[1], li[2]];
+	}
+	matches.push([li[7], li[8], li[9], li[5]+li[6]]);
+}
+if (matches.length) push_perf_exons(matches, last);
+
+// for each gene, count how many primary exons are perfect
+var pg_aux_cnt = {};
+for (var e = 0; e < perf_exons.length; ++e) {
+	if (!pri_exon[e]) continue;
+	var pe = perf_exons[e];
+	var n = pe? pe.length : 0;
+	for (var i = 0; i < n; ++i) {
+		var g = pe[i];
+		if (pg_aux_cnt[g] == null) pg_aux_cnt[g] = 1;
+		else ++pg_aux_cnt[g];
+	}
+}
+
+// find genes with perfect matches on the primary exons
+var perf_genes = [];
+for (var g in pg_aux_cnt)
+	if (pg_aux_cnt[g] == n_pri_exons)
+		perf_genes.push(parseInt(g));
+warn("- Found " +perf_genes.length+ " genes fully covered by perfect matches on the primary exon(s)");
+
+var h_perf_genes = {};
+for (var i = 0; i < perf_genes.length; ++i) {
+	if (dbg) print("PG", glist[perf_genes[i]]);
+	h_perf_genes[perf_genes[i]] = true;
+}
+
+/*******************
+ * Filter hit list *
+ *******************/
+
+// reorganize hits to exons
+function list2exons(list, flt_flag, perf_hash)
+{
+	var exons = [];
+	for (var i = 0; i < list.length; ++i) {
+		var li = list[i], c = chash[li[0]], g = ghash[li[1]];
+		if (flt_flag != null && flt_flag[c] == 1) continue;
+		if (perf_hash != null && !perf_hash[g]) continue;
+		if (exons[li[2]] == null) exons[li[2]] = [];
+		exons[li[2]].push([c, g, li[5] + li[6], li[4] - li[3]]);
+	}
+	return exons;
+}
+
+var exons = list2exons(list), flt_flag = [], ovlp_len = [];
+for (var c = 0; c < clist.length; ++c) flt_flag[c] = ovlp_len[c] = 0;
+for (var e = 0; e < exons.length; ++e) {
+	if (!pri_exon[e]) continue;
+	var ee = exons[e];
+	var max_len = [];
+	for (var c = 0; c < clist.length; ++c) max_len[c] = 0;
+	for (var i = 0; i < ee.length; ++i) {
+		var l = ee[i][3] - ee[i][2];
+		if (l < 1) l = 1;
+		if (max_len[ee[i][0]] < l) max_len[ee[i][0]] = l;
+	}
+	for (var c = 0; c < clist.length; ++c) ovlp_len[c] += max_len[c];
+	for (var i = 0; i < ee.length; ++i)
+		flt_flag[ee[i][0]] |= (!h_perf_genes[ee[i][1]] || ee[i][2])? 1 : 1<<1;	
+}
+
+var l_cons = 0, l_incons = 0;
+for (var c = 0; c < clist.length; ++c)
+	if (flt_flag[c]&2) l_cons += ovlp_len[c];
+	else if (flt_flag[c] == 1) l_incons += ovlp_len[c];
+
+warn("- Total length of contigs consistent/inconsistent with perfect genes: " +l_cons+ "/" +l_incons);
+var attempt_perf = (l_incons/(l_cons+l_incons) < thres_frac);
+
+/********************************
+ * Core function for genotyping *
+ ********************************/
+
+function type_gene(perf_mode)
+{
+	if (perf_mode) {
+		var flt_list = [];
+		for (var c = 0; c < clist.length; ++c)
+			if (flt_flag[c] == 1) flt_list.push(clist[c]);
+		warn("  - Filtered " +flt_list.length+ " inconsistent contig(s): [" +flt_list.join(",")+ "]");
+		exons = list2exons(list, flt_flag, h_perf_genes);
+	} else exons = list2exons(list);
+
+	/***********************
+	 * Score each genotype *
+	 ***********************/
+
+	// initialize genotype scores
+	var pair = [];
+	for (var i = 0; i < glist.length; ++i) {
+		pair[i] = [];
+		for (var j = 0; j <= i; ++j)
+			pair[i][j] = 0;
+	}
+
+	// these two arrays are used to output debugging information
+	var score = [], ctg = [];
+
+	function type_exon(e, gt_list)
+	{
+		function update_pair(x, m, is_pri)
+		{
+			var y, z;
+			y = (x>>14&0xff) + m < 0xff? (x>>14&0xff) + m : 0xff;
+			if (is_pri) z = (x>>22) + m < 0xff? (x>>22) + m : 0xff;
+			else z = x>>22;
+			return z<<22 | y<<14 | ((x&0x3fff) + (1<<6|is_pri));
+		}
+
+		score[e] = []; ctg[e] = [];
+		if (exons[e] == null) return;
+		var ee = exons[e], is_pri = pri_exon[e]? 1 : 0;
+		// find contigs and genes associated with the current exon
+		var ch = {}, gh = {};
+		for (var i = 0; i < ee.length; ++i)
+			if (elist[ee[i][1]][e] != null)
+				ch[ee[i][0]] = true, gh[ee[i][1]] = true;
+		var ga = [], ca = ctg[e];
+		for (var c in ch) ca.push(parseInt(c));
+		for (var g in gh) ga.push(parseInt(g));
+		var named_ca = [];
+		for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]);
+		warn("    - Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
+		// set unmapped entries to high mismatch
+		var sc = score[e];
+		for (var k = 0; k < ga.length; ++k) {
+			var g = ga[k];
+			if (sc[g] == null) sc[g] = [];
+			for (var i = 0; i < ca.length; ++i)
+				sc[g][ca[i]] = 0xff;
+		}
+		// convert representation again and compute max_len[]
+		var max_len = [];
+		for (var i = 0; i < ee.length; ++i) {
+			var c = ee[i][0], g = ee[i][1];
+			if (gh[g] == null || ch[c] == null) continue;
+			sc[g][c] = sc[g][c] < ee[i][2]? sc[g][c] : ee[i][2];
+			if (max_len[c] == null) max_len[c] = 0;
+			max_len[c] = max_len[c] > ee[i][3]? max_len[c] : ee[i][3];
+		}
+		// drop mismapped contigs
+		var max_max_len = 0;
+		for (var k = 0; k < ca.length; ++k)
+			max_max_len = max_max_len > max_len[ca[k]]? max_max_len : max_len[ca[k]];
+		var dropped = [];
+		for (var k = 0; k < ca.length; ++k) {
+			var min = 0x7fffffff, c = ca[k];
+			for (var i = 0; i < ga.length; ++i) {
+				var g = ga[i];
+				min = min < sc[g][c]? min : sc[g][c];
+			}
+			dropped[c] = min > thres_nm? true : false;
+			if (max_len[c] < thres_len && max_len[c] < thres_ratio * max_max_len) dropped[c] = true;
+			if (dropped[c]) warn("      . Dropped low-quality contig " +clist[c]+ " (minNM=" +min+ "; maxLen=" +max_len[c]+ ")");
+		}
+		// fill the pair array
+		if (gt_list == null) {
+			for (var i = 0; i < ga.length; ++i) {
+				var m = 0, gi = ga[i], g1 = sc[gi];
+				// homozygous
+				for (var k = 0; k < ca.length; ++k) {
+					var c = ca[k];
+					if (!dropped[c]) m += g1[c];
+				}
+				pair[gi][gi] = update_pair(pair[gi][gi], m, is_pri);
+				// heterozygous
+				for (var j = i + 1; j < ga.length; ++j) {
+					var gj = ga[j], g2 = sc[gj], m = 0, a = [0, 0];
+					for (var k = 0; k < ca.length; ++k) {
+						var c = ca[k];
+						if (!dropped[c]) {
+							m += g1[c] < g2[c]? g1[c] : g2[c];
+							++a[g1[c]<g2[c]? 0:1];
+						}
+					}
+					if (a[0] == 0 || a[1] == 0) m = 0xff; // if all contigs are assigned to one gene, it is not good
+					if (gi < gj) pair[gj][gi] = update_pair(pair[gj][gi], m, is_pri);
+					else pair[gi][gj] = update_pair(pair[gi][gj], m, is_pri);
+				}
+			}
+		} else {
+			var tmp_pairs = [], min = 0xff;
+			for (var i = 0; i < gt_list.length; ++i) {
+				var gt = gt_list[i], m = 0;
+				var g1 = sc[gt[0]], g2 = sc[gt[1]], a = [0, 0];
+				if (g1 == null || g2 == null) continue;
+				if (gt[0] == gt[1]) {
+					for (var k = 0; k < ca.length; ++k) {
+						var c = ca[k];
+						if (!dropped[c]) m += g1[c];
+					}
+				} else {
+					var a = [0, 0];
+					for (k = 0; k < ca.length; ++k) {
+						var c = ca[k];
+						if (!dropped[c]) {
+							m += g1[c] < g2[c]? g1[c] : g2[c];
+							++a[g1[c]<g2[c]? 0:1];
+						}
+					}
+					if (a[0] == 0 || a[1] == 0) m = 0xff;
+				}
+				tmp_pairs.push([gt[0], gt[1], m]);
+				min = min < m? min : m;
+			}
+			if (min < 0xff) {
+				for (var i = 0; i < tmp_pairs.length; ++i) {
+					var t = tmp_pairs[i];
+					pair[t[0]][t[1]] = update_pair(pair[t[0]][t[1]], t[2], is_pri);
+				}
+			} else warn("      . Skipped exon " +(e+1)+ " as the assembly may be incomplete");
+		}
+	}
+
+	// type primary exons
+	warn("  - Processing primary exon(s)...");
+	for (var e = 0; e < exons.length; ++e)
+		if (pri_exon[e]) type_exon(e);
+
+	// generate the list of best genotypes on primary exons
+	var min_nm_pri = 0x7fffffff;
+	for (var i = 0; i < glist.length; ++i)
+		for (var j = 0; j <= i; ++j)
+			if ((pair[i][j]&63) == n_pri_exons)
+				min_nm_pri = min_nm_pri < pair[i][j]>>22? min_nm_pri : pair[i][j]>>22;
+
+	var gt_list = [];
+	for (var i = 0; i < glist.length; ++i)
+		for (var j = 0; j <= i; ++j)
+			if ((pair[i][j]&63) == n_pri_exons && pair[i][j]>>22 == min_nm_pri)
+				gt_list.push([i, j]);
+
+	warn("  - Collected " +gt_list.length+ " top genotypes on the primary exon(s); minimal edit distance: " +min_nm_pri);
+
+	// type other exons
+	warn("  - Processing other exon(s)...");
+	for (var e = 0; e < exons.length; ++e)
+		if (!pri_exon[e]) type_exon(e, gt_list);
+
+	/*****************************
+	 * Choose the best genotypes *
+	 *****************************/
+
+	// genotyping
+	var min_nm = 0x7fffffff;
+	for (var i = 0; i < glist.length; ++i)
+		for (var j = 0; j <= i; ++j)
+			if ((pair[i][j]&63) == n_pri_exons)
+				min_nm = min_nm < pair[i][j]>>14? min_nm : pair[i][j]>>14;
+
+	var out = [];
+	for (var i = 0; i < glist.length; ++i)
+		for (var j = 0; j <= i; ++j)
+			if ((pair[i][j]&63) == n_pri_exons && pair[i][j]>>14 <= min_nm + 1)
+				out.push([pair[i][j]>>14, pair[i][j]>>6&0xff, i, j, (gsuf[i] + gsuf[j])<<16|(gsub[i] + gsub[j])]);
+
+	out.sort(function(a, b) { return a[0]!=b[0]? a[0]-b[0] : a[1]!=b[1]? b[1]-a[1] : a[4]!=b[4]? a[4]-b[4] : a[2]!=b[2]? a[2]-b[2] : a[3]-b[3]});
+
+	return out;
+}
+
+/**********************
+ * Perform genotyping *
+ **********************/
+
+warn("- Typing in the imperfect mode...");
+var rst = type_gene(false);
+if (attempt_perf) {
+	warn("- Typing in the perfect mode...");
+	var rst_perf = type_gene(true);
+	warn("- Imperfect vs perfect mode: [" +(rst[0][0]>>8&0xff)+ "," +(rst[0][0]&0xff)+ "] vs [" +(rst_perf[0][0]>>8&0xff)+ "," +(rst_perf[0][0]&0xff)+ "]");
+	if (rst_perf[0][0] < rst[0][0]) {
+		warn("- Chose the result from the perfect mode");
+		rst = rst_perf;
+	} else warn("- Chose the result from the imperfect mode");
+} else warn("- Perfect mode is not attempted");
+
+/**********
+ * Output *
+ **********/
+
+for (var i = 0; i < rst.length; ++i)
+	print("GT", glist[rst[i][3]], glist[rst[i][2]], rst[i][0]>>8&0xff, rst[i][0]&0xff, rst[i][1]);

bwakit/typeHLA.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+is_ctg=0
+
+if [ $# -gt 1 ] && [ $1 == '-A' ]; then
+	is_ctg=1
+	shift
+fi
+
+if [ $# -lt 2 ]; then
+	echo "Usage: $0 [-A] <prefix> <gene>"
+	exit 1
+fi
+
+preres="resource-human-HLA"
+root=`dirname $0`
+pre=$1.$2
+touch $pre.gt
+
+if [ ! -s $pre.fq ]; then
+	echo '** Empty input file. Abort!' >&2
+	exit 0
+fi
+
+if [ $is_ctg -eq 0 ]; then
+	echo "** De novo assembling..." >&2
+	len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
+	$root/fermi2.pl unitig -f $root/fermi2 -r $root/ropebwt2 -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
+	make -f $pre.tmp.mak >&2
+	cp $pre.tmp.mag.gz $pre.mag.gz
+else
+	rm -f $pre.tmp.mag.gz
+	ln -s $pre.fq $pre.tmp.mag.gz
+fi
+
+echo "** Selecting contigs overlapping target exons..." >&2
+(ls $root/$preres/HLA-ALT-idx/*.fa.bwt | sed s,.bwt,, | xargs -i $root/bwa mem -t2 -B1 -O1 -E1 {} $pre.tmp.mag.gz 2>/dev/null) | grep -v ^@ | sort -k3,3 -k4,4n | gzip > $pre.tmp.ALT.sam.gz
+$root/k8 $root/typeHLA-selctg.js $2 $root/$preres/HLA-ALT-exons.bed $pre.tmp.ALT.sam.gz | $root/seqtk subseq $pre.tmp.mag.gz - | gzip -1 > $pre.tmp.fq.gz
+
+echo "** Mapping exons to de novo contigs..." >&2
+$root/bwa index -p $pre.tmp $pre.tmp.fq.gz 2>/dev/null
+$root/seqtk comp $root/$preres/HLA-CDS.fa | cut -f1 | grep ^$2 | $root/seqtk subseq $root/$preres/HLA-CDS.fa - | $root/bwa mem -aD.1 -t2 $pre.tmp - 2>/dev/null | gzip -1 > $pre.sam.gz
+
+echo "** Typing..." >&2
+$root/k8 $root/typeHLA.js $pre.sam.gz > $pre.gt
+
+# delete temporary files
+rm -f $pre.tmp.*
+[ $is_ctg -eq 1 ] && rm -f $pre.mag.gz

bwamem.h

@@ -0,0 +1,213 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#ifndef BWAMEM_H_
+#define BWAMEM_H_
+
+#include "bwt.h"
+#include "bntseq.h"
+#include "bwa.h"
+
+#define MEM_MAPQ_COEF 30.0
+#define MEM_MAPQ_MAX  60
+
+struct __smem_i;
+typedef struct __smem_i smem_i;
+
+#define MEM_F_PE        0x2
+#define MEM_F_NOPAIRING 0x4
+#define MEM_F_ALL       0x8
+#define MEM_F_NO_MULTI  0x10
+#define MEM_F_NO_RESCUE 0x20
+#define MEM_F_REF_HDR	0x100
+#define MEM_F_SOFTCLIP  0x200
+#define MEM_F_SMARTPE   0x400
+#define MEM_F_PRIMARY5  0x800
+#define MEM_F_KEEP_SUPP_MAPQ 0x1000
+#define MEM_F_XB        0x2000
+
+typedef struct {
+	int a, b;               // match score and mismatch penalty
+	int o_del, e_del;
+	int o_ins, e_ins;
+	int pen_unpaired;       // phred-scaled penalty for unpaired reads
+	int pen_clip5,pen_clip3;// clipping penalty. This score is not deducted from the DP score.
+	int w;                  // band width
+	int zdrop;              // Z-dropoff
+
+	uint64_t max_mem_intv;
+
+	int T;                  // output score threshold; only affecting output
+	int flag;               // see MEM_F_* macros
+	int min_seed_len;       // minimum seed length
+	int min_chain_weight;
+	int max_chain_extend;
+	float split_factor;     // split into a seed if MEM is longer than min_seed_len*split_factor
+	int split_width;        // split into a seed if its occurence is smaller than this value
+	int max_occ;            // skip a seed if its occurence is larger than this value
+	int max_chain_gap;      // do not chain seed if it is max_chain_gap-bp away from the closest seed
+	int n_threads;          // number of threads
+	int chunk_size;         // process chunk_size-bp sequences in a batch
+	float mask_level;       // regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
+	float drop_ratio;       // drop a chain if its seed coverage is below drop_ratio times the seed coverage of a better chain overlapping with the small chain
+	float XA_drop_ratio;    // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
+	float mask_level_redun;
+	float mapQ_coef_len;
+	int mapQ_coef_fac;
+	int max_ins;            // when estimating insert size distribution, skip pairs with insert longer than this value
+	int max_matesw;         // perform maximally max_matesw rounds of mate-SW for each end
+	int max_XA_hits, max_XA_hits_alt; // if there are max_hits or fewer, output them all
+	int8_t mat[25];         // scoring matrix; mat[0] == 0 if unset
+} mem_opt_t;
+
+typedef struct {
+	int64_t rb, re; // [rb,re): reference sequence in the alignment
+	int qb, qe;     // [qb,qe): query sequence in the alignment
+	int rid;        // reference seq ID
+	int score;      // best local SW score
+	int truesc;     // actual score corresponding to the aligned region; possibly smaller than $score
+	int sub;        // 2nd best SW score
+	int alt_sc;
+	int csub;       // SW score of a tandem hit
+	int sub_n;      // approximate number of suboptimal hits
+	int w;          // actual band width used in extension
+	int seedcov;    // length of regions coverged by seeds
+	int secondary;  // index of the parent hit shadowing the current hit; <0 if primary
+	int secondary_all;
+	int seedlen0;   // length of the starting seed
+	int n_comp:30, is_alt:2; // number of sub-alignments chained together
+	float frac_rep;
+	uint64_t hash;
+} mem_alnreg_t;
+
+typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
+
+typedef struct {
+	int low, high;   // lower and upper bounds within which a read pair is considered to be properly paired
+	int failed;      // non-zero if the orientation is not supported by sufficient data
+	double avg, std; // mean and stddev of the insert size distribution
+} mem_pestat_t;
+
+typedef struct { // This struct is only used for the convenience of API.
+	int64_t pos;     // forward strand 5'-end mapping position
+	int rid;         // reference sequence index in bntseq_t; <0 for unmapped
+	int flag;        // extra flag
+	uint32_t is_rev:1, is_alt:1, mapq:8, NM:22; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance
+	int n_cigar;     // number of CIGAR operations
+	uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234
+	char *XA;        // alternative mappings
+
+	int score, sub, alt_sc;
+} mem_aln_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	smem_i *smem_itr_init(const bwt_t *bwt);
+	void smem_itr_destroy(smem_i *itr);
+	void smem_set_query(smem_i *itr, int len, const uint8_t *query);
+	void smem_config(smem_i *itr, int min_intv, int max_len, uint64_t max_intv);
+	const bwtintv_v *smem_next(smem_i *itr);
+
+	mem_opt_t *mem_opt_init(void);
+	void mem_fill_scmat(int a, int b, int8_t mat[25]);
+
+	/**
+	 * Align a batch of sequences and generate the alignments in the SAM format
+	 *
+	 * This routine requires $seqs[i].{l_seq,seq,name} and write $seqs[i].sam.
+	 * Note that $seqs[i].sam may consist of several SAM lines if the
+	 * corresponding sequence has multiple primary hits.
+	 *
+	 * In the paired-end mode (i.e. MEM_F_PE is set in $opt->flag), query
+	 * sequences must be interleaved: $n must be an even number and the 2i-th
+	 * sequence and the (2i+1)-th sequence constitute a read pair. In this
+	 * mode, there should be enough (typically >50) unique pairs for the
+	 * routine to infer the orientation and insert size.
+	 *
+	 * @param opt    alignment parameters
+	 * @param bwt    FM-index of the reference sequence
+	 * @param bns    Information of the reference
+	 * @param pac    2-bit encoded reference
+	 * @param n      number of query sequences
+	 * @param seqs   query sequences; $seqs[i].seq/sam to be modified after the call
+	 * @param pes0   insert-size info; if NULL, infer from data; if not NULL, it should be an array with 4 elements,
+	 *               corresponding to each FF, FR, RF and RR orientation. See mem_pestat() for more info.
+	 */
+	void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int64_t n_processed, int n, bseq1_t *seqs, const mem_pestat_t *pes0);
+
+	/**
+	 * Find the aligned regions for one query sequence
+	 *
+	 * Note that this routine does not generate CIGAR. CIGAR should be
+	 * generated later by mem_reg2aln() below.
+	 *
+	 * @param opt    alignment parameters
+	 * @param bwt    FM-index of the reference sequence
+	 * @param bns    Information of the reference
+	 * @param pac    2-bit encoded reference
+	 * @param l_seq  length of query sequence
+	 * @param seq    query sequence
+	 *
+	 * @return       list of aligned regions.
+	 */
+	mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq);
+
+	/**
+	 * Generate CIGAR and forward-strand position from alignment region
+	 *
+	 * @param opt    alignment parameters
+	 * @param bns    Information of the reference
+	 * @param pac    2-bit encoded reference
+	 * @param l_seq  length of query sequence
+	 * @param seq    query sequence
+	 * @param ar     one alignment region
+	 *
+	 * @return       CIGAR, strand, mapping quality and forward-strand position
+	 */
+	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq, const mem_alnreg_t *ar);
+	mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq, const mem_alnreg_t *ar, const char *name);
+
+	/**
+	 * Infer the insert size distribution from interleaved alignment regions
+	 *
+	 * This function can be called after mem_align1(), as long as paired-end
+	 * reads are properly interleaved.
+	 *
+	 * @param opt    alignment parameters
+	 * @param l_pac  length of concatenated reference sequence
+	 * @param n      number of query sequences; must be an even number
+	 * @param regs   region array of size $n; 2i-th and (2i+1)-th elements constitute a pair
+	 * @param pes    inferred insert size distribution (output)
+	 */
+	void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwamem_extra.c

@@ -0,0 +1,172 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <limits.h>
+#include "bwa.h"
+#include "bwamem.h"
+#include "bntseq.h"
+#include "kstring.h"
+
+/***************************
+ * SMEM iterator interface *
+ ***************************/
+
+struct __smem_i {
+	const bwt_t *bwt;
+	const uint8_t *query;
+	int start, len;
+	int min_intv, max_len;
+	uint64_t max_intv;
+	bwtintv_v *matches; // matches; to be returned by smem_next()
+	bwtintv_v *sub;     // sub-matches inside the longest match; temporary
+	bwtintv_v *tmpvec[2]; // temporary arrays
+};
+
+smem_i *smem_itr_init(const bwt_t *bwt)
+{
+	smem_i *itr;
+	itr = calloc(1, sizeof(smem_i));
+	itr->bwt = bwt;
+	itr->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
+	itr->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
+	itr->matches   = calloc(1, sizeof(bwtintv_v));
+	itr->sub       = calloc(1, sizeof(bwtintv_v));
+	itr->min_intv = 1;
+	itr->max_len  = INT_MAX;
+	itr->max_intv = 0;
+	return itr;
+}
+
+void smem_itr_destroy(smem_i *itr)
+{
+	free(itr->tmpvec[0]->a); free(itr->tmpvec[0]);
+	free(itr->tmpvec[1]->a); free(itr->tmpvec[1]);
+	free(itr->matches->a);   free(itr->matches);
+	free(itr->sub->a);       free(itr->sub);
+	free(itr);
+}
+
+void smem_set_query(smem_i *itr, int len, const uint8_t *query)
+{
+	itr->query = query;
+	itr->start = 0;
+	itr->len = len;
+}
+
+void smem_config(smem_i *itr, int min_intv, int max_len, uint64_t max_intv)
+{
+	itr->min_intv = min_intv;
+	itr->max_len  = max_len;
+	itr->max_intv = max_intv;
+}
+
+const bwtintv_v *smem_next(smem_i *itr)
+{
+	int ori_start;
+	itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = itr->sub->n = 0;
+	if (itr->start >= itr->len || itr->start < 0) return 0;
+	while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases
+	if (itr->start == itr->len) return 0;
+	ori_start = itr->start;
+	itr->start = bwt_smem1a(itr->bwt, itr->len, itr->query, ori_start, itr->min_intv, itr->max_intv, itr->matches, itr->tmpvec); // search for SMEM
+	return itr->matches;
+}
+
+/***********************
+ *** Extra functions ***
+ ***********************/
+
+mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq_)
+{ // the difference from mem_align1_core() is that this routine: 1) calls mem_mark_primary_se(); 2) does not modify the input sequence
+	extern mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq, void *buf);
+	extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
+	mem_alnreg_v ar;
+	char *seq;
+	seq = malloc(l_seq);
+	memcpy(seq, seq_, l_seq); // makes a copy of seq_
+	ar = mem_align1_core(opt, bwt, bns, pac, l_seq, seq, 0);
+	mem_mark_primary_se(opt, ar.n, ar.a, lrand48());
+	free(seq);
+	return ar;
+}
+
+static inline int get_pri_idx(double XA_drop_ratio, const mem_alnreg_t *a, int i)
+{
+	int k = a[i].secondary_all;
+	if (k >= 0 && a[i].score >= a[k].score * XA_drop_ratio) return k;
+	return -1;
+}
+
+// Okay, returning strings is bad, but this has happened a lot elsewhere. If I have time, I need serious code cleanup.
+char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query) // ONLY work after mem_mark_primary_se()
+{
+	int i, k, r, *cnt, tot;
+	kstring_t *aln = 0, str = {0,0,0};
+	char **XA = 0, *has_alt;
+
+	cnt = calloc(a->n, sizeof(int));
+	has_alt = calloc(a->n, 1);
+	for (i = 0, tot = 0; i < a->n; ++i) {
+		r = get_pri_idx(opt->XA_drop_ratio, a->a, i);
+		if (r >= 0) {
+			++cnt[r], ++tot;
+			if (a->a[i].is_alt) has_alt[r] = 1;
+		}
+	}
+	if (tot == 0) goto end_gen_alt;
+	aln = calloc(a->n, sizeof(kstring_t));
+	for (i = 0; i < a->n; ++i) {
+		mem_aln_t t;
+		if ((r = get_pri_idx(opt->XA_drop_ratio, a->a, i)) < 0) continue;
+		if (cnt[r] > opt->max_XA_hits_alt || (!has_alt[r] && cnt[r] > opt->max_XA_hits)) continue;
+		t = mem_reg2aln(opt, bns, pac, l_query, query, &a->a[i]);
+		str.l = 0;
+		kputs(bns->anns[t.rid].name, &str);
+		kputc(',', &str); kputc("+-"[t.is_rev], &str); kputl(t.pos + 1, &str);
+		kputc(',', &str);
+		for (k = 0; k < t.n_cigar; ++k) {
+			kputw(t.cigar[k]>>4, &str);
+			kputc("MIDSHN"[t.cigar[k]&0xf], &str);
+		}
+		kputc(',', &str); kputw(t.NM, &str);
+		if (opt->flag & MEM_F_XB) {
+			kputc(',', &str);
+			kputw(t.score, &str);
+			kputc(',', &str);
+			kputw(t.mapq, &str);
+		}
+		kputc(';', &str);
+		free(t.cigar);
+		kputsn(str.s, str.l, &aln[r]);
+	}
+	XA = calloc(a->n, sizeof(char*));
+	for (k = 0; k < a->n; ++k)
+		XA[k] = aln[k].s;
+
+end_gen_alt:
+	free(has_alt); free(cnt); free(aln); free(str.s);
+	return XA;
+}

bwamem_pair.c

@@ -0,0 +1,419 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
+#include "kstring.h"
+#include "bwamem.h"
+#include "kvec.h"
+#include "utils.h"
+#include "ksw.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
+#define MIN_RATIO     0.8
+#define MIN_DIR_CNT   10
+#define MIN_DIR_RATIO 0.05
+#define OUTLIER_BOUND 2.0
+#define MAPPING_BOUND 3.0
+#define MAX_STDDEV    4.0
+
+static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
+{
+	int64_t p2;
+	int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
+	p2 = r1 == r2? b2 : (l_pac<<1) - 1 - b2; // p2 is the coordinate of read 2 on the read 1 strand
+	*dist = p2 > b1? p2 - b1 : b1 - p2;
+	return (r1 == r2? 0 : 1) ^ (p2 > b1? 0 : 3);
+}
+
+static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
+{
+	int j;
+	for (j = 1; j < r->n; ++j) { // choose unique alignment
+		int b_max = r->a[j].qb > r->a[0].qb? r->a[j].qb : r->a[0].qb;
+		int e_min = r->a[j].qe < r->a[0].qe? r->a[j].qe : r->a[0].qe;
+		if (e_min > b_max) { // have overlap
+			int min_l = r->a[j].qe - r->a[j].qb < r->a[0].qe - r->a[0].qb? r->a[j].qe - r->a[j].qb : r->a[0].qe - r->a[0].qb;
+			if (e_min - b_max >= min_l * opt->mask_level) break; // significant overlap
+		}
+	}
+	return j < r->n? r->a[j].score : opt->min_seed_len * opt->a;
+}
+
+void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4])
+{
+	int i, d, max;
+	uint64_v isize[4];
+	memset(pes, 0, 4 * sizeof(mem_pestat_t));
+	memset(isize, 0, sizeof(kvec_t(int)) * 4);
+	for (i = 0; i < n>>1; ++i) {
+		int dir;
+		int64_t is;
+		mem_alnreg_v *r[2];
+		r[0] = (mem_alnreg_v*)&regs[i<<1|0];
+		r[1] = (mem_alnreg_v*)&regs[i<<1|1];
+		if (r[0]->n == 0 || r[1]->n == 0) continue;
+		if (cal_sub(opt, r[0]) > MIN_RATIO * r[0]->a[0].score) continue;
+		if (cal_sub(opt, r[1]) > MIN_RATIO * r[1]->a[0].score) continue;
+		if (r[0]->a[0].rid != r[1]->a[0].rid) continue; // not on the same chr
+		dir = mem_infer_dir(l_pac, r[0]->a[0].rb, r[1]->a[0].rb, &is);
+		if (is && is <= opt->max_ins) kv_push(uint64_t, isize[dir], is);
+	}
+	if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
+	for (d = 0; d < 4; ++d) { // TODO: this block is nearly identical to the one in bwtsw2_pair.c. It would be better to merge these two.
+		mem_pestat_t *r = &pes[d];
+		uint64_v *q = &isize[d];
+		int p25, p50, p75, x;
+		if (q->n < MIN_DIR_CNT) {
+			fprintf(stderr, "[M::%s] skip orientation %c%c as there are not enough pairs\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
+			r->failed = 1;
+			free(q->a);
+			continue;
+		} else fprintf(stderr, "[M::%s] analyzing insert size distribution for orientation %c%c...\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
+		ks_introsort_64(q->n, q->a);
+		p25 = q->a[(int)(.25 * q->n + .499)];
+		p50 = q->a[(int)(.50 * q->n + .499)];
+		p75 = q->a[(int)(.75 * q->n + .499)];
+		r->low  = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
+		if (r->low < 1) r->low = 1;
+		r->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
+		fprintf(stderr, "[M::%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
+		fprintf(stderr, "[M::%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r->low, r->high);
+		for (i = x = 0, r->avg = 0; i < q->n; ++i)
+			if (q->a[i] >= r->low && q->a[i] <= r->high)
+				r->avg += q->a[i], ++x;
+		r->avg /= x;
+		for (i = 0, r->std = 0; i < q->n; ++i)
+			if (q->a[i] >= r->low && q->a[i] <= r->high)
+				r->std += (q->a[i] - r->avg) * (q->a[i] - r->avg);
+		r->std = sqrt(r->std / x);
+		fprintf(stderr, "[M::%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r->avg, r->std);
+		r->low  = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
+		r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
+		if (r->low  > r->avg - MAX_STDDEV * r->std) r->low  = (int)(r->avg - MAX_STDDEV * r->std + .499);
+		if (r->high < r->avg + MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
+		if (r->low < 1) r->low = 1;
+		fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
+		free(q->a);
+	}
+	for (d = 0, max = 0; d < 4; ++d)
+		max = max > isize[d].n? max : isize[d].n;
+	for (d = 0; d < 4; ++d)
+		if (pes[d].failed == 0 && isize[d].n < max * MIN_DIR_RATIO) {
+			pes[d].failed = 1;
+			fprintf(stderr, "[M::%s] skip orientation %c%c\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
+		}
+}
+
+int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
+{
+	extern int mem_sort_dedup_patch(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int n, mem_alnreg_t *a);
+	int64_t l_pac = bns->l_pac;
+	int i, r, skip[4], n = 0, rid;
+	for (r = 0; r < 4; ++r)
+		skip[r] = pes[r].failed? 1 : 0;
+	for (i = 0; i < ma->n; ++i) { // check which orinentation has been found
+		int64_t dist;
+		r = mem_infer_dir(l_pac, a->rb, ma->a[i].rb, &dist);
+		if (dist >= pes[r].low && dist <= pes[r].high)
+			skip[r] = 1;
+	}
+	if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW
+	for (r = 0; r < 4; ++r) {
+		int is_rev, is_larger;
+		uint8_t *seq, *rev = 0, *ref = 0;
+		int64_t rb, re;
+		if (skip[r]) continue;
+		is_rev = (r>>1 != (r&1)); // whether to reverse complement the mate
+		is_larger = !(r>>1); // whether the mate has larger coordinate
+		if (is_rev) {
+			rev = malloc(l_ms); // this is the reverse complement of $ms
+			for (i = 0; i < l_ms; ++i) rev[l_ms - 1 - i] = ms[i] < 4? 3 - ms[i] : 4;
+			seq = rev;
+		} else seq = (uint8_t*)ms;
+		if (!is_rev) {
+			rb = is_larger? a->rb + pes[r].low : a->rb - pes[r].high;
+			re = (is_larger? a->rb + pes[r].high: a->rb - pes[r].low) + l_ms; // if on the same strand, end position should be larger to make room for the seq length
+		} else {
+			rb = (is_larger? a->rb + pes[r].low : a->rb - pes[r].high) - l_ms; // similarly on opposite strands
+			re = is_larger? a->rb + pes[r].high: a->rb - pes[r].low;
+		}
+		if (rb < 0) rb = 0;
+		if (re > l_pac<<1) re = l_pac<<1;
+		if (rb < re) ref = bns_fetch_seq(bns, pac, &rb, (rb+re)>>1, &re, &rid);
+		if (a->rid == rid && re - rb >= opt->min_seed_len) { // no funny things happening
+			kswr_t aln;
+			mem_alnreg_t b;
+			int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
+			aln = ksw_align2(l_ms, seq, re - rb, ref, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, xtra, 0);
+			memset(&b, 0, sizeof(mem_alnreg_t));
+			if (aln.score >= opt->min_seed_len && aln.qb >= 0) { // something goes wrong if aln.qb < 0
+				b.rid = a->rid;
+				b.is_alt = a->is_alt;
+				b.qb = is_rev? l_ms - (aln.qe + 1) : aln.qb;                                                                                                                                                                              
+				b.qe = is_rev? l_ms - aln.qb : aln.qe + 1; 
+				b.rb = is_rev? (l_pac<<1) - (rb + aln.te + 1) : rb + aln.tb;
+				b.re = is_rev? (l_pac<<1) - (rb + aln.tb) : rb + aln.te + 1;
+				b.score = aln.score;
+				b.csub = aln.score2;
+				b.secondary = -1;
+				b.seedcov = (b.re - b.rb < b.qe - b.qb? b.re - b.rb : b.qe - b.qb) >> 1;
+//				printf("*** %d, [%lld,%lld], %d:%d, (%lld,%lld), (%lld,%lld) == (%lld,%lld)\n", aln.score, rb, re, is_rev, is_larger, a->rb, a->re, ma->a[0].rb, ma->a[0].re, b.rb, b.re);
+				kv_push(mem_alnreg_t, *ma, b); // make room for a new element
+				// move b s.t. ma is sorted
+				for (i = 0; i < ma->n - 1; ++i) // find the insertion point
+					if (ma->a[i].score < b.score) break;
+				tmp = i;
+				for (i = ma->n - 1; i > tmp; --i) ma->a[i] = ma->a[i-1];
+				ma->a[i] = b;
+			}
+			++n;
+		}
+		if (n) ma->n = mem_sort_dedup_patch(opt, 0, 0, 0, ma->n, ma->a);
+		if (rev) free(rev);
+		free(ref);
+	}
+	return n;
+}
+
+int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id, int *sub, int *n_sub, int z[2], int n_pri[2])
+{
+	pair64_v v, u;
+	int r, i, k, y[4], ret; // y[] keeps the last hit
+	int64_t l_pac = bns->l_pac;
+	kv_init(v); kv_init(u);
+	for (r = 0; r < 2; ++r) { // loop through read number
+		for (i = 0; i < n_pri[r]; ++i) {
+			pair64_t key;
+			mem_alnreg_t *e = &a[r].a[i];
+			key.x = e->rb < l_pac? e->rb : (l_pac<<1) - 1 - e->rb; // forward position
+			key.x = (uint64_t)e->rid<<32 | (key.x - bns->anns[e->rid].offset);
+			key.y = (uint64_t)e->score << 32 | i << 2 | (e->rb >= l_pac)<<1 | r;
+			kv_push(pair64_t, v, key);
+		}
+	}
+	ks_introsort_128(v.n, v.a);
+	y[0] = y[1] = y[2] = y[3] = -1;
+	//for (i = 0; i < v.n; ++i) printf("[%d]\t%d\t%c%ld\n", i, (int)(v.a[i].y&1)+1, "+-"[v.a[i].y>>1&1], (long)v.a[i].x);
+	for (i = 0; i < v.n; ++i) {
+		for (r = 0; r < 2; ++r) { // loop through direction
+			int dir = r<<1 | (v.a[i].y>>1&1), which;
+			if (pes[dir].failed) continue; // invalid orientation
+			which = r<<1 | ((v.a[i].y&1)^1);
+			if (y[which] < 0) continue; // no previous hits
+			for (k = y[which]; k >= 0; --k) { // TODO: this is a O(n^2) solution in the worst case; remember to check if this loop takes a lot of time (I doubt)
+				int64_t dist;
+				int q;
+				double ns;
+				pair64_t *p;
+				if ((v.a[k].y&3) != which) continue;
+				dist = (int64_t)v.a[i].x - v.a[k].x;
+				//printf("%d: %lld\n", k, dist);
+				if (dist > pes[dir].high) break;
+				if (dist < pes[dir].low)  continue;
+				ns = (dist - pes[dir].avg) / pes[dir].std;
+				q = (int)((v.a[i].y>>32) + (v.a[k].y>>32) + .721 * log(2. * erfc(fabs(ns) * M_SQRT1_2)) * opt->a + .499); // .721 = 1/log(4)
+				if (q < 0) q = 0;
+				p = kv_pushp(pair64_t, u);
+				p->y = (uint64_t)k<<32 | i;
+				p->x = (uint64_t)q<<32 | (hash_64(p->y ^ id<<8) & 0xffffffffU);
+				//printf("[%lld,%lld]\t%d\tdist=%ld\n", v.a[k].x, v.a[i].x, q, (long)dist);
+			}
+		}
+		y[v.a[i].y&3] = i;
+	}
+	if (u.n) { // found at least one proper pair
+		int tmp = opt->a + opt->b;
+		tmp = tmp > opt->o_del + opt->e_del? tmp : opt->o_del + opt->e_del;
+		tmp = tmp > opt->o_ins + opt->e_ins? tmp : opt->o_ins + opt->e_ins;
+		ks_introsort_128(u.n, u.a);
+		i = u.a[u.n-1].y >> 32; k = u.a[u.n-1].y << 32 >> 32;
+		z[v.a[i].y&1] = v.a[i].y<<32>>34; // index of the best pair
+		z[v.a[k].y&1] = v.a[k].y<<32>>34;
+		ret = u.a[u.n-1].x >> 32;
+		*sub = u.n > 1? u.a[u.n-2].x>>32 : 0;
+		for (i = (long)u.n - 2, *n_sub = 0; i >= 0; --i)
+			if (*sub - (int)(u.a[i].x>>32) <= tmp) ++*n_sub;
+	} else ret = 0, *sub = 0, *n_sub = 0;
+	free(u.a); free(v.a);
+	return ret;
+}
+
+void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
+void mem_reorder_primary5(int T, mem_alnreg_v *a);
+
+#define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
+
+int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
+{
+	extern int mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
+	extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
+	extern void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
+	extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
+
+	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2], n_aa[2];
+	kstring_t str;
+	mem_aln_t h[2], g[2], aa[2][2];
+
+	str.l = str.m = 0; str.s = 0;
+	memset(h, 0, sizeof(mem_aln_t) * 2);
+	memset(g, 0, sizeof(mem_aln_t) * 2);
+	n_aa[0] = n_aa[1] = 0;
+	if (!(opt->flag & MEM_F_NO_RESCUE)) { // then perform SW for the best alignment
+		mem_alnreg_v b[2];
+		kv_init(b[0]); kv_init(b[1]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < a[i].n; ++j)
+				if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
+					kv_push(mem_alnreg_t, b[i], a[i].a[j]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
+				n += mem_matesw(opt, bns, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
+		free(b[0].a); free(b[1].a);
+	}
+	n_pri[0] = mem_mark_primary_se(opt, a[0].n, a[0].a, id<<1|0);
+	n_pri[1] = mem_mark_primary_se(opt, a[1].n, a[1].a, id<<1|1);
+	if (opt->flag & MEM_F_PRIMARY5) {
+		mem_reorder_primary5(opt->T, &a[0]);
+		mem_reorder_primary5(opt->T, &a[1]);
+	}
+	if (opt->flag&MEM_F_NOPAIRING) goto no_pairing;
+	// pairing single-end hits
+	if (n_pri[0] && n_pri[1] && (o = mem_pair(opt, bns, pac, pes, s, a, id, &subo, &n_sub, z, n_pri)) > 0) {
+		int is_multi[2], q_pe, score_un, q_se[2];
+		char **XA[2];
+		// check if an end has multiple hits even after mate-SW
+		for (i = 0; i < 2; ++i) {
+			for (j = 1; j < n_pri[i]; ++j)
+				if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break;
+			is_multi[i] = j < n_pri[i]? 1 : 0;
+		}
+		if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score
+		// compute mapQ for the best SE hit
+		score_un = a[0].a[0].score + a[1].a[0].score - opt->pen_unpaired;
+		//q_pe = o && subo < o? (int)(MEM_MAPQ_COEF * (1. - (double)subo / o) * log(a[0].a[z[0]].seedcov + a[1].a[z[1]].seedcov) + .499) : 0;
+		subo = subo > score_un? subo : score_un;
+		q_pe = raw_mapq(o - subo, opt->a);
+		if (n_sub > 0) q_pe -= (int)(4.343 * log(n_sub+1) + .499);
+		if (q_pe < 0) q_pe = 0;
+		if (q_pe > 60) q_pe = 60;
+		q_pe = (int)(q_pe * (1. - .5 * (a[0].a[0].frac_rep + a[1].a[0].frac_rep)) + .499);
+		// the following assumes no split hits
+		if (o > score_un) { // paired alignment is preferred
+			mem_alnreg_t *c[2];
+			c[0] = &a[0].a[z[0]]; c[1] = &a[1].a[z[1]];
+			for (i = 0; i < 2; ++i) {
+				if (c[i]->secondary >= 0)
+					c[i]->sub = a[i].a[c[i]->secondary].score, c[i]->secondary = -2;
+				q_se[i] = mem_approx_mapq_se(opt, c[i]);
+			}
+			q_se[0] = q_se[0] > q_pe? q_se[0] : q_pe < q_se[0] + 40? q_pe : q_se[0] + 40;
+			q_se[1] = q_se[1] > q_pe? q_se[1] : q_pe < q_se[1] + 40? q_pe : q_se[1] + 40;
+			extra_flag |= 2;
+			// cap at the tandem repeat score
+			q_se[0] = q_se[0] < raw_mapq(c[0]->score - c[0]->csub, opt->a)? q_se[0] : raw_mapq(c[0]->score - c[0]->csub, opt->a);
+			q_se[1] = q_se[1] < raw_mapq(c[1]->score - c[1]->csub, opt->a)? q_se[1] : raw_mapq(c[1]->score - c[1]->csub, opt->a);
+		} else { // the unpaired alignment is preferred
+			z[0] = z[1] = 0;
+			q_se[0] = mem_approx_mapq_se(opt, &a[0].a[0]);
+			q_se[1] = mem_approx_mapq_se(opt, &a[1].a[0]);
+		}
+		for (i = 0; i < 2; ++i) {
+			int k = a[i].a[z[i]].secondary_all;
+			if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
+				assert(a[i].a[k].secondary_all < 0);
+				for (j = 0; j < a[i].n; ++j)
+					if (a[i].a[j].secondary_all == k || j == k)
+						a[i].a[j].secondary_all = z[i];
+				a[i].a[z[i]].secondary_all = -1;
+			}
+		}
+		if (!(opt->flag & MEM_F_ALL)) {
+			for (i = 0; i < 2; ++i)
+				XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
+		} else XA[0] = XA[1] = 0;
+		// write SAM
+		for (i = 0; i < 2; ++i) {
+			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[z[i]]);
+			h[i].mapq = q_se[i];
+			h[i].flag |= 0x40<<i | extra_flag;
+			h[i].XA = XA[i]? XA[i][z[i]] : 0;
+			aa[i][n_aa[i]++] = h[i];
+			if (n_pri[i] < a[i].n) { // the read has ALT hits
+				mem_alnreg_t *p = &a[i].a[n_pri[i]];
+				if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) continue;
+				g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, p);
+				g[i].flag |= 0x800 | 0x40<<i | extra_flag;
+				g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
+				aa[i][n_aa[i]++] = g[i];
+			}
+		}
+		for (i = 0; i < n_aa[0]; ++i)
+			mem_aln2sam(opt, bns, &str, &s[0], n_aa[0], aa[0], i, &h[1]); // write read1 hits
+		s[0].sam = strdup(str.s); str.l = 0;
+		for (i = 0; i < n_aa[1]; ++i)
+			mem_aln2sam(opt, bns, &str, &s[1], n_aa[1], aa[1], i, &h[0]); // write read2 hits
+		s[1].sam = str.s;
+		if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
+		// free
+		for (i = 0; i < 2; ++i) {
+			free(h[i].cigar); free(g[i].cigar);
+			if (XA[i] == 0) continue;
+			for (j = 0; j < a[i].n; ++j) free(XA[i][j]);
+			free(XA[i]);
+		}
+	} else goto no_pairing;
+	return n;
+
+no_pairing:
+	for (i = 0; i < 2; ++i) {
+		int which = -1;
+		if (a[i].n) {
+			if (a[i].a[0].score >= opt->T) which = 0;
+			else if (n_pri[i] < a[i].n && a[i].a[n_pri[i]].score >= opt->T)
+				which = n_pri[i];
+		}
+		if (which >= 0) h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[which]);
+		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
+	}
+	if (!(opt->flag & MEM_F_NOPAIRING) && h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
+		int64_t dist;
+		int d;
+		d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
+		if (!pes[d].failed && dist >= pes[d].low && dist <= pes[d].high) extra_flag |= 2;
+	}
+	mem_reg2sam(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
+	mem_reg2sam(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
+	if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
+	free(h[0].cigar); free(h[1].cigar);
+	return n;
+}

bwape.c

@@ -0,0 +1,784 @@
+#include <unistd.h>
+#include <math.h>
+#include <stdlib.h>
+#include <time.h>
+#include <stdio.h>
+#include <string.h>
+#include "bwtaln.h"
+#include "kvec.h"
+#include "bntseq.h"
+#include "utils.h"
+#include "bwase.h"
+#include "bwa.h"
+#include "ksw.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef struct {
+	int n;
+	bwtint_t *a;
+} poslist_t;
+
+typedef struct {
+	double avg, std, ap_prior;
+	bwtint_t low, high, high_bayesian;
+} isize_info_t;
+
+#define b128_eq(a, b) ((a).x == (b).x && (a).y == (b).y)
+#define b128_hash(a) ((uint32_t)(a).x)
+
+#include "khash.h"
+KHASH_INIT(b128, pair64_t, poslist_t, 1, b128_hash, b128_eq)
+
+typedef struct {
+	pair64_v arr;
+	pair64_v pos[2];
+	kvec_t(bwt_aln1_t) aln[2];
+} pe_data_t;
+
+#define MIN_HASH_WIDTH 1000
+
+extern int g_log_n[256]; // in bwase.c
+static kh_b128_t *g_hash;
+
+void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi);
+void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
+int bwa_approx_mapQ(const bwa_seq_t *p, int mm);
+void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
+bntseq_t *bwa_open_nt(const char *prefix);
+void bwa_print_sam_SQ(const bntseq_t *bns);
+
+pe_opt_t *bwa_init_pe_opt()
+{
+	pe_opt_t *po;
+	po = (pe_opt_t*)calloc(1, sizeof(pe_opt_t));
+	po->max_isize = 500;
+	po->force_isize = 0;
+	po->max_occ = 100000;
+	po->n_multi = 3;
+	po->N_multi = 10;
+	po->type = BWA_PET_STD;
+	po->is_sw = 1;
+	po->ap_prior = 1e-5;
+	return po;
+}
+/*
+static double ierfc(double x) // inverse erfc(); iphi(x) = M_SQRT2 *ierfc(2 * x);
+{
+	const double a = 0.140012;
+	double b, c;
+	b = log(x * (2 - x));
+	c = 2./M_PI/a + b / 2.;
+	return sqrt(sqrt(c * c - b / a) - c);
+}
+*/
+
+// for normal distribution, this is about 3std
+#define OUTLIER_BOUND 2.0
+
+static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double ap_prior, int64_t L)
+{
+	uint64_t x, *isizes, n_ap = 0;
+	int n, i, tot, p25, p75, p50, max_len = 1, tmp;
+	double skewness = 0.0, kurtosis = 0.0, y;
+
+	ii->avg = ii->std = -1.0;
+	ii->low = ii->high = ii->high_bayesian = 0;
+	isizes = (uint64_t*)calloc(n_seqs, 8);
+	for (i = 0, tot = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p[2];
+		p[0] = seqs[0] + i; p[1] = seqs[1] + i;
+		if (p[0]->mapQ >= 20 && p[1]->mapQ >= 20) {
+			x = (p[0]->pos < p[1]->pos)? p[1]->pos + p[1]->len - p[0]->pos : p[0]->pos + p[0]->len - p[1]->pos;
+			if (x < 100000) isizes[tot++] = x;
+		}
+		if (p[0]->len > max_len) max_len = p[0]->len;
+		if (p[1]->len > max_len) max_len = p[1]->len;
+	}
+	if (tot < 20) {
+		fprintf(stderr, "[infer_isize] fail to infer insert size: too few good pairs\n");
+		free(isizes);
+		return -1;
+	}
+	ks_introsort_64(tot, isizes);
+	p25 = isizes[(int)(tot*0.25 + 0.5)];
+	p50 = isizes[(int)(tot*0.50 + 0.5)];
+	p75 = isizes[(int)(tot*0.75 + 0.5)];
+	tmp  = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
+	ii->low = tmp > max_len? tmp : max_len; // ii->low is unsigned
+	ii->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
+	if (ii->low > ii->high) {
+		fprintf(stderr, "[infer_isize] fail to infer insert size: upper bound is smaller than read length\n");
+		free(isizes);
+		return -1;
+	}
+	for (i = 0, x = n = 0; i < tot; ++i)
+		if (isizes[i] >= ii->low && isizes[i] <= ii->high)
+			++n, x += isizes[i];
+	ii->avg = (double)x / n;
+	for (i = 0; i < tot; ++i) {
+		if (isizes[i] >= ii->low && isizes[i] <= ii->high) {
+			double tmp = (isizes[i] - ii->avg) * (isizes[i] - ii->avg);
+			ii->std += tmp;
+			skewness += tmp * (isizes[i] - ii->avg);
+			kurtosis += tmp * tmp;
+		}
+	}
+	kurtosis = kurtosis/n / (ii->std / n * ii->std / n) - 3;
+	ii->std = sqrt(ii->std / n); // it would be better as n-1, but n is usually very large
+	skewness = skewness / n / (ii->std * ii->std * ii->std);
+	for (y = 1.0; y < 10.0; y += 0.01)
+		if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
+	ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
+	for (i = 0; i < tot; ++i)
+		if (isizes[i] > ii->high_bayesian) ++n_ap;
+	ii->ap_prior = .01 * (n_ap + .01) / tot;
+	if (ii->ap_prior < ap_prior) ii->ap_prior = ap_prior;
+	free(isizes);
+	fprintf(stderr, "[infer_isize] (25, 50, 75) percentile: (%d, %d, %d)\n", p25, p50, p75);
+	if (isnan(ii->std) || p75 > 100000) {
+		ii->low = ii->high = ii->high_bayesian = 0; ii->avg = ii->std = -1.0;
+		fprintf(stderr, "[infer_isize] fail to infer insert size: weird pairing\n");
+		return -1;
+	}
+	for (y = 1.0; y < 10.0; y += 0.01)
+		if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
+	ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
+	fprintf(stderr, "[infer_isize] low and high boundaries: %ld and %ld for estimating avg and std\n", (long)ii->low, (long)ii->high);
+	fprintf(stderr, "[infer_isize] inferred external isize from %d pairs: %.3lf +/- %.3lf\n", n, ii->avg, ii->std);
+	fprintf(stderr, "[infer_isize] skewness: %.3lf; kurtosis: %.3lf; ap_prior: %.2e\n", skewness, kurtosis, ii->ap_prior);
+	fprintf(stderr, "[infer_isize] inferred maximum insert size: %ld (%.2lf sigma)\n", (long)ii->high_bayesian, y);
+	return 0;
+}
+
+static int pairing(bwa_seq_t *p[2], pe_data_t *d, const pe_opt_t *opt, int s_mm, const isize_info_t *ii)
+{
+	int i, j, o_n, subo_n, cnt_chg = 0, low_bound = ii->low, max_len;
+	uint64_t o_score, subo_score;
+	pair64_t last_pos[2][2], o_pos[2];
+	max_len = p[0]->full_len;
+	if (max_len < p[1]->full_len) max_len = p[1]->full_len;
+	if (low_bound < max_len) low_bound = max_len;
+
+	// here v>=u. When ii is set, we check insert size with ii; otherwise with opt->max_isize
+#define __pairing_aux(u,v) do { \
+		bwtint_t l = (v).x + p[(v).y&1]->len - ((u).x); \
+		if ((u).x != (uint64_t)-1 && (v).x > (u).x && l >= max_len \
+			&& ((ii->high && l <= ii->high_bayesian) || (ii->high == 0 && l <= opt->max_isize))) \
+		{ \
+			uint64_t s = d->aln[(v).y&1].a[(v).y>>2].score + d->aln[(u).y&1].a[(u).y>>2].score; \
+			s *= 10; \
+			if (ii->high) s += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * fabs(l - ii->avg) / ii->std)) + .499); \
+			s = s<<32 | (uint32_t)hash_64((u).x<<32 | (v).x); \
+			if (s>>32 == o_score>>32) ++o_n; \
+			else if (s>>32 < o_score>>32) { subo_n += o_n; o_n = 1; } \
+			else ++subo_n; \
+			if (s < o_score) subo_score = o_score, o_score = s, o_pos[(u).y&1] = (u), o_pos[(v).y&1] = (v); \
+			else if (s < subo_score) subo_score = s; \
+		} \
+	} while (0)
+
+#define __pairing_aux2(q, w) do { \
+		const bwt_aln1_t *r = d->aln[(w).y&1].a + ((w).y>>2); \
+		(q)->extra_flag |= SAM_FPP; \
+		if ((q)->pos != (w).x || (q)->strand != ((w).y>>1&1)) { \
+			(q)->n_mm = r->n_mm; (q)->n_gapo = r->n_gapo; (q)->n_gape = r->n_gape; (q)->strand = (w).y>>1&1; \
+			(q)->score = r->score; \
+			(q)->pos = (w).x; \
+			if ((q)->mapQ > 0) ++cnt_chg; \
+		} \
+	} while (0)
+
+	o_score = subo_score = (uint64_t)-1;
+	o_n = subo_n = 0;
+	ks_introsort_128(d->arr.n, d->arr.a);
+	for (j = 0; j < 2; ++j) last_pos[j][0].x = last_pos[j][0].y = last_pos[j][1].x = last_pos[j][1].y = (uint64_t)-1;
+	if (opt->type == BWA_PET_STD) {
+		for (i = 0; i < d->arr.n; ++i) {
+			pair64_t x = d->arr.a[i];
+			int strand = x.y>>1&1;
+			if (strand == 1) { // reverse strand, then check
+				int y = 1 - (x.y&1);
+				__pairing_aux(last_pos[y][1], x);
+				__pairing_aux(last_pos[y][0], x);
+			} else { // forward strand, then push
+				last_pos[x.y&1][0] = last_pos[x.y&1][1];
+				last_pos[x.y&1][1] = x;
+			}
+		}
+	} else {
+		fprintf(stderr, "[paring] not implemented yet!\n");
+		exit(1);
+	}
+	// set pairing
+	//fprintf(stderr, "[%ld, %d, %d, %d]\n", d->arr.n, (int)(o_score>>32), (int)(subo_score>>32), o_n);
+	if (o_score != (uint64_t)-1) {
+		int mapQ_p = 0; // this is the maximum mapping quality when one end is moved
+		//fprintf(stderr, "%d, %d\n", o_n, subo_n);
+		if (o_n == 1) {
+			if (subo_score == (uint64_t)-1) mapQ_p = 29; // no sub-optimal pair
+			else if ((subo_score>>32) - (o_score>>32) > s_mm * 10) mapQ_p = 23; // poor sub-optimal pair
+			else {
+				int n = subo_n > 255? 255 : subo_n;
+				mapQ_p = ((subo_score>>32) - (o_score>>32)) / 2 - g_log_n[n];
+				if (mapQ_p < 0) mapQ_p = 0;
+			}
+		}
+		if ((p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) && (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1))) { // both ends not moved
+			if (p[0]->mapQ > 0 && p[1]->mapQ > 0) {
+				int mapQ = p[0]->mapQ + p[1]->mapQ;
+				if (mapQ > 60) mapQ = 60;
+				p[0]->mapQ = p[1]->mapQ = mapQ;
+			} else {
+				if (p[0]->mapQ == 0) p[0]->mapQ = (mapQ_p + 7 < p[1]->mapQ)? mapQ_p + 7 : p[1]->mapQ;
+				if (p[1]->mapQ == 0) p[1]->mapQ = (mapQ_p + 7 < p[0]->mapQ)? mapQ_p + 7 : p[0]->mapQ;
+			}
+		} else if (p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) { // [1] moved
+			p[1]->seQ = 0; p[1]->mapQ = p[0]->mapQ;
+			if (p[1]->mapQ > mapQ_p) p[1]->mapQ = mapQ_p;
+		} else if (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1)) { // [0] moved
+			p[0]->seQ = 0; p[0]->mapQ = p[1]->mapQ;
+			if (p[0]->mapQ > mapQ_p) p[0]->mapQ = mapQ_p;
+		} else { // both ends moved
+			p[0]->seQ = p[1]->seQ = 0;
+			mapQ_p -= 20;
+			if (mapQ_p < 0) mapQ_p = 0;
+			p[0]->mapQ = p[1]->mapQ = mapQ_p;
+		}
+		__pairing_aux2(p[0], o_pos[0]);
+		__pairing_aux2(p[1], o_pos[1]);
+	}
+	return cnt_chg;
+}
+
+typedef struct {
+	kvec_t(bwt_aln1_t) aln;
+} aln_buf_t;
+
+int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bwt, int n_seqs, bwa_seq_t *seqs[2], FILE *fp_sa[2], isize_info_t *ii,
+					   const pe_opt_t *opt, const gap_opt_t *gopt, const isize_info_t *last_ii)
+{
+	int i, j, cnt_chg = 0;
+	char str[1024];
+	bwt_t *bwt;
+	pe_data_t *d;
+	aln_buf_t *buf[2];
+
+	d = (pe_data_t*)calloc(1, sizeof(pe_data_t));
+	buf[0] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));
+	buf[1] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));
+
+	if (_bwt == 0) { // load forward SA
+		strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
+		strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
+	} else bwt = _bwt;
+
+	// SE
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p[2];
+		for (j = 0; j < 2; ++j) {
+			int n_aln;
+			p[j] = seqs[j] + i;
+			p[j]->n_multi = 0;
+			p[j]->extra_flag |= SAM_FPD | (j == 0? SAM_FR1 : SAM_FR2);
+			err_fread_noeof(&n_aln, 4, 1, fp_sa[j]);
+			if (n_aln > kv_max(d->aln[j]))
+				kv_resize(bwt_aln1_t, d->aln[j], n_aln);
+			d->aln[j].n = n_aln;
+			err_fread_noeof(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
+			kv_copy(bwt_aln1_t, buf[j][i].aln, d->aln[j]); // backup d->aln[j]
+			// generate SE alignment and mapping quality
+			bwa_aln2seq(n_aln, d->aln[j].a, p[j]);
+			if (p[j]->type == BWA_TYPE_UNIQUE || p[j]->type == BWA_TYPE_REPEAT) {
+				int strand;
+				int max_diff = gopt->fnr > 0.0? bwa_cal_maxdiff(p[j]->len, BWA_AVG_ERR, gopt->fnr) : gopt->max_diff;
+				p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
+				p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len + p[j]->ref_shift, &strand);
+				p[j]->strand = strand;
+				if (p[j]->pos == (bwtint_t)-1) p[j]->type = BWA_TYPE_NO_MATCH;
+			}
+		}
+	}
+
+	// infer isize
+	infer_isize(n_seqs, seqs, ii, opt->ap_prior, bwt->seq_len/2);
+	if (ii->avg < 0.0 && last_ii->avg > 0.0) *ii = *last_ii;
+	if (opt->force_isize) {
+		fprintf(stderr, "[%s] discard insert size estimate as user's request.\n", __func__);
+		ii->low = ii->high = 0; ii->avg = ii->std = -1.0;
+	}
+
+	// PE
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p[2];
+		for (j = 0; j < 2; ++j) {
+			p[j] = seqs[j] + i;
+			kv_copy(bwt_aln1_t, d->aln[j], buf[j][i].aln);
+		}
+		if ((p[0]->type == BWA_TYPE_UNIQUE || p[0]->type == BWA_TYPE_REPEAT)
+			&& (p[1]->type == BWA_TYPE_UNIQUE || p[1]->type == BWA_TYPE_REPEAT))
+		{ // only when both ends mapped
+			pair64_t x;
+			int j, k;
+			long long n_occ[2];
+			for (j = 0; j < 2; ++j) {
+				n_occ[j] = 0;
+				for (k = 0; k < d->aln[j].n; ++k)
+					n_occ[j] += d->aln[j].a[k].l - d->aln[j].a[k].k + 1;
+			}
+			if (n_occ[0] > opt->max_occ || n_occ[1] > opt->max_occ) continue;
+			d->arr.n = 0;
+			for (j = 0; j < 2; ++j) {
+				for (k = 0; k < d->aln[j].n; ++k) {
+					bwt_aln1_t *r = d->aln[j].a + k;
+					bwtint_t l;
+					if (0 && r->l - r->k + 1 >= MIN_HASH_WIDTH) { // then check hash table
+						pair64_t key;
+						int ret;
+						key.x = r->k; key.y = r->l;
+						khint_t iter = kh_put(b128, g_hash, key, &ret);
+						if (ret) { // not in the hash table; ret must equal 1 as we never remove elements
+							poslist_t *z = &kh_val(g_hash, iter);
+							z->n = r->l - r->k + 1;
+							z->a = (bwtint_t*)malloc(sizeof(bwtint_t) * z->n);
+							for (l = r->k; l <= r->l; ++l) {
+								int strand;
+								z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand)<<1;
+								z->a[l - r->k] |= strand;
+							}
+						}
+						for (l = 0; l < kh_val(g_hash, iter).n; ++l) {
+							x.x = kh_val(g_hash, iter).a[l]>>1;
+							x.y = k<<2 | (kh_val(g_hash, iter).a[l]&1)<<1 | j;
+							kv_push(pair64_t, d->arr, x);
+						}
+					} else { // then calculate on the fly
+						for (l = r->k; l <= r->l; ++l) {
+							int strand;
+							x.x = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand);
+							x.y = k<<2 | strand<<1 | j;
+							kv_push(pair64_t, d->arr, x);
+						}
+					}
+				}
+			}
+			cnt_chg += pairing(p, d, opt, gopt->s_mm, ii);
+		}
+
+		if (opt->N_multi || opt->n_multi) {
+			for (j = 0; j < 2; ++j) {
+				if (p[j]->type != BWA_TYPE_NO_MATCH) {
+					int k, n_multi;
+					if (!(p[j]->extra_flag&SAM_FPP) && p[1-j]->type != BWA_TYPE_NO_MATCH) {
+						bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, p[j]->c1+p[j]->c2-1 > opt->N_multi? opt->n_multi : opt->N_multi);
+					} else bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, opt->n_multi);
+					for (k = 0, n_multi = 0; k < p[j]->n_multi; ++k) {
+						int strand;
+						bwt_multi1_t *q = p[j]->multi + k;
+						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
+						q->strand = strand;
+						if (q->pos != p[j]->pos && q->pos != (bwtint_t)-1)
+							p[j]->multi[n_multi++] = *q;
+					}
+					p[j]->n_multi = n_multi;
+				}
+			}
+		}
+	}
+
+	// free
+	for (i = 0; i < n_seqs; ++i) {
+		kv_destroy(buf[0][i].aln);
+		kv_destroy(buf[1][i].aln);
+	}
+	free(buf[0]); free(buf[1]);
+	if (_bwt == 0) bwt_destroy(bwt);
+	kv_destroy(d->arr);
+	kv_destroy(d->pos[0]); kv_destroy(d->pos[1]);
+	kv_destroy(d->aln[0]); kv_destroy(d->aln[1]);
+	free(d);
+	return cnt_chg;
+}
+
+#define SW_MIN_MATCH_LEN 20
+#define SW_MIN_MAPQ 17
+
+// cnt = n_mm<<16 | n_gapo<<8 | n_gape
+bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen, int *n_cigar, uint32_t *_cnt)
+{
+	kswr_t r;
+	uint32_t *cigar32 = 0;
+	bwa_cigar_t *cigar = 0;
+	ubyte_t *ref_seq;
+	bwtint_t k, x, y, l;
+	int xtra, gscore;
+	int8_t mat[25];
+
+	bwa_fill_scmat(1, 3, mat);
+	// check whether there are too many N's
+	if (reglen < SW_MIN_MATCH_LEN || (int64_t)l_pac - *beg < len) return 0;
+	for (k = 0, x = 0; k < len; ++k)
+		if (seq[k] >= 4) ++x;
+	if ((float)x/len >= 0.25 || len - x < SW_MIN_MATCH_LEN) return 0;
+
+	// get reference subsequence
+	ref_seq = (ubyte_t*)calloc(reglen, 1);
+	for (k = *beg, l = 0; l < reglen && k < l_pac; ++k)
+		ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
+
+	// do alignment
+	xtra = KSW_XSUBO | KSW_XSTART | (len < 250? KSW_XBYTE : 0);
+	r = ksw_align(len, (uint8_t*)seq, l, ref_seq, 5, mat, 5, 1, xtra, 0);
+	gscore = ksw_global(r.qe - r.qb + 1, &seq[r.qb], r.te - r.tb + 1, &ref_seq[r.tb], 5, mat, 5, 1, 50, n_cigar, &cigar32);
+	cigar = (bwa_cigar_t*)cigar32;
+	for (k = 0; k < *n_cigar; ++k)
+		cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
+
+	if (r.score < SW_MIN_MATCH_LEN || r.score2 == r.score || gscore != r.score) { // poor hit or tandem hits or weird alignment
+		free(cigar); free(ref_seq); *n_cigar = 0;
+		return 0;
+	}
+
+	// check whether the alignment is good enough
+	for (k = 0, x = y = 0; k < *n_cigar; ++k) {
+		bwa_cigar_t c = cigar[k];
+		if (__cigar_op(c) == FROM_M) x += __cigar_len(c), y += __cigar_len(c);
+		else if (__cigar_op(c) == FROM_D) x += __cigar_len(c);
+		else y += __cigar_len(c);
+	}
+	if (x < SW_MIN_MATCH_LEN || y < SW_MIN_MATCH_LEN) { // not good enough
+		free(cigar); free(ref_seq);
+		*n_cigar = 0;
+		return 0;
+	}
+
+	{ // update cigar and coordinate;
+		int start = r.qb, end = r.qe + 1;
+		*beg += r.tb;
+		cigar = (bwa_cigar_t*)realloc(cigar, sizeof(bwa_cigar_t) * (*n_cigar + 2));
+		if (start) {
+			memmove(cigar + 1, cigar, sizeof(bwa_cigar_t) * (*n_cigar));
+			cigar[0] = __cigar_create(3, start);
+			++(*n_cigar);
+		}
+		if (end < len) {
+			/*cigar[*n_cigar] = 3<<14 | (len - end);*/
+			cigar[*n_cigar] = __cigar_create(3, (len - end));
+			++(*n_cigar);
+		}
+	}
+
+	{ // set *cnt
+		int n_mm, n_gapo, n_gape;
+		n_mm = n_gapo = n_gape = 0;
+		x = r.tb; y = r.qb;
+		for (k = 0; k < *n_cigar; ++k) {
+			bwa_cigar_t c = cigar[k];
+			if (__cigar_op(c) == FROM_M) {
+				for (l = 0; l < (__cigar_len(c)); ++l)
+					if (ref_seq[x+l] < 4 && seq[y+l] < 4 && ref_seq[x+l] != seq[y+l]) ++n_mm;
+				x += __cigar_len(c), y += __cigar_len(c);
+			} else if (__cigar_op(c) == FROM_D) {
+				x += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
+			} else if (__cigar_op(c) == FROM_I) {
+				y += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
+			}
+		}
+		*_cnt = (uint32_t)n_mm<<16 | n_gapo<<8 | n_gape;
+	}
+	
+	free(ref_seq);
+	return cigar;
+}
+
+ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs, bwa_seq_t *seqs[2], const pe_opt_t *popt, const isize_info_t *ii)
+{
+	ubyte_t *pacseq;
+	int i;
+	uint64_t n_tot[2], n_mapped[2];
+
+	// load reference sequence
+	if (_pacseq == 0) {
+		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
+		err_rewind(bns->fp_pac);
+		err_fread_noeof(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
+	} else pacseq = (ubyte_t*)_pacseq;
+	if (!popt->is_sw || ii->avg < 0.0) return pacseq;
+
+	// perform mate alignment
+	n_tot[0] = n_tot[1] = n_mapped[0] = n_mapped[1] = 0;
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p[2];
+		p[0] = seqs[0] + i; p[1] = seqs[1] + i;
+		if ((p[0]->mapQ >= SW_MIN_MAPQ || p[1]->mapQ >= SW_MIN_MAPQ) && (p[0]->extra_flag&SAM_FPP) == 0) { // unpaired and one read has high mapQ
+			int k, n_cigar[2], is_singleton, mapQ = 0, mq_adjust[2];
+			int64_t beg[2], end[2];
+			bwa_cigar_t *cigar[2];
+			uint32_t cnt[2];
+
+			/* In the following, _pref points to the reference read
+			 * which must be aligned; _pmate points to its mate which is
+			 * considered to be modified. */
+
+#define __set_rght_coor(_a, _b, _pref, _pmate) do {						\
+				(_a) = (int64_t)_pref->pos + ii->avg - 3 * ii->std - _pmate->len * 1.5; \
+				(_b) = (_a) + 6 * ii->std + 2 * _pmate->len;			\
+				if ((_a) < (int64_t)_pref->pos + _pref->len) (_a) = _pref->pos + _pref->len; \
+				if ((_b) > bns->l_pac) (_b) = bns->l_pac;				\
+			} while (0)
+
+#define __set_left_coor(_a, _b, _pref, _pmate) do {						\
+				(_a) = (int64_t)_pref->pos + _pref->len - ii->avg - 3 * ii->std - _pmate->len * 0.5; \
+				(_b) = (_a) + 6 * ii->std + 2 * _pmate->len;			\
+				if ((_a) < 0) (_a) = 0;									\
+				if ((_b) > _pref->pos) (_b) = _pref->pos;				\
+			} while (0)
+			
+#define __set_fixed(_pref, _pmate, _beg, _cnt) do {						\
+				_pmate->type = BWA_TYPE_MATESW;							\
+				_pmate->pos = _beg;										\
+				_pmate->seQ = _pref->seQ;								\
+				_pmate->strand = (popt->type == BWA_PET_STD)? 1 - _pref->strand : _pref->strand; \
+				_pmate->n_mm = _cnt>>16; _pmate->n_gapo = _cnt>>8&0xff; _pmate->n_gape = _cnt&0xff; \
+				_pmate->extra_flag |= SAM_FPP;							\
+				_pref->extra_flag |= SAM_FPP;							\
+			} while (0)
+
+			mq_adjust[0] = mq_adjust[1] = 255; // not effective
+			is_singleton = (p[0]->type == BWA_TYPE_NO_MATCH || p[1]->type == BWA_TYPE_NO_MATCH)? 1 : 0;
+
+			++n_tot[is_singleton];
+			cigar[0] = cigar[1] = 0;
+			n_cigar[0] = n_cigar[1] = 0;
+			if (popt->type != BWA_PET_STD) continue; // other types of pairing is not considered
+			for (k = 0; k < 2; ++k) { // p[1-k] is the reference read and p[k] is the read considered to be modified
+				ubyte_t *seq;
+				if (p[1-k]->type == BWA_TYPE_NO_MATCH) continue; // if p[1-k] is unmapped, skip
+				{ // note that popt->type == BWA_PET_STD always true; in older versions, there was a branch for color-space FF/RR reads
+					if (p[1-k]->strand == 0) { // then the mate is on the reverse strand and has larger coordinate
+						__set_rght_coor(beg[k], end[k], p[1-k], p[k]);
+						seq = p[k]->rseq;
+					} else { // then the mate is on forward stand and has smaller coordinate
+						__set_left_coor(beg[k], end[k], p[1-k], p[k]);
+						seq = p[k]->seq;
+						seq_reverse(p[k]->len, seq, 0); // because ->seq is reversed; this will reversed back shortly
+					}
+				}
+				// perform SW alignment
+				cigar[k] = bwa_sw_core(bns->l_pac, pacseq, p[k]->len, seq, &beg[k], end[k] - beg[k], &n_cigar[k], &cnt[k]);
+				if (cigar[k] && p[k]->type != BWA_TYPE_NO_MATCH) { // re-evaluate cigar[k]
+					int s_old, clip = 0, s_new;
+					if (__cigar_op(cigar[k][0]) == 3) clip += __cigar_len(cigar[k][0]);
+					if (__cigar_op(cigar[k][n_cigar[k]-1]) == 3) clip += __cigar_len(cigar[k][n_cigar[k]-1]);
+					s_old = (int)((p[k]->n_mm * 9 + p[k]->n_gapo * 13 + p[k]->n_gape * 2) / 3. * 8. + .499);
+					s_new = (int)(((cnt[k]>>16) * 9 + (cnt[k]>>8&0xff) * 13 + (cnt[k]&0xff) * 2 + clip * 3) / 3. * 8. + .499);
+					s_old += -4.343 * log(ii->ap_prior / bns->l_pac);
+					s_new += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * 1.5) + .499)); // assume the mapped isize is 1.5\sigma
+					if (s_old < s_new) { // reject SW alignment
+						mq_adjust[k] = s_new - s_old;
+						free(cigar[k]); cigar[k] = 0; n_cigar[k] = 0;
+					} else mq_adjust[k] = s_old - s_new;
+				}
+				// now revserse sequence back such that p[*]->seq looks untouched
+				if (popt->type == BWA_PET_STD) {
+					if (p[1-k]->strand == 1) seq_reverse(p[k]->len, seq, 0);
+				} else {
+					if (p[1-k]->strand == 0) seq_reverse(p[k]->len, seq, 0);
+				}
+			}
+			k = -1; // no read to be changed
+			if (cigar[0] && cigar[1]) {
+				k = p[0]->mapQ < p[1]->mapQ? 0 : 1; // p[k] to be fixed
+				mapQ = abs(p[1]->mapQ - p[0]->mapQ);
+			} else if (cigar[0]) k = 0, mapQ = p[1]->mapQ;
+			else if (cigar[1]) k = 1, mapQ = p[0]->mapQ;
+			if (k >= 0 && p[k]->pos != beg[k]) {
+				++n_mapped[is_singleton];
+				{ // recalculate mapping quality
+					int tmp = (int)p[1-k]->mapQ - p[k]->mapQ/2 - 8;
+					if (tmp <= 0) tmp = 1;
+					if (mapQ > tmp) mapQ = tmp;
+					p[k]->mapQ = p[1-k]->mapQ = mapQ;
+					p[k]->seQ = p[1-k]->seQ = p[1-k]->seQ < mapQ? p[1-k]->seQ : mapQ;
+					if (p[k]->mapQ > mq_adjust[k]) p[k]->mapQ = mq_adjust[k];
+					if (p[k]->seQ > mq_adjust[k]) p[k]->seQ = mq_adjust[k];
+				}
+				// update CIGAR
+				free(p[k]->cigar); p[k]->cigar = cigar[k]; cigar[k] = 0;
+				p[k]->n_cigar = n_cigar[k];
+				// update the rest of information
+				__set_fixed(p[1-k], p[k], beg[k], cnt[k]);
+			}
+			free(cigar[0]); free(cigar[1]);
+		}
+	}
+	fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d singletons are mated.\n",
+			(long long)n_mapped[1], (long long)n_tot[1], SW_MIN_MAPQ);
+	fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d discordant pairs are fixed.\n",
+			(long long)n_mapped[0], (long long)n_tot[0], SW_MIN_MAPQ);
+	return pacseq;
+}
+
+void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line)
+{
+	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
+	int i, j, n_seqs;
+	long long tot_seqs = 0;
+	bwa_seq_t *seqs[2];
+	bwa_seqio_t *ks[2];
+	clock_t t;
+	bntseq_t *bns;
+	FILE *fp_sa[2];
+	gap_opt_t opt, opt0;
+	khint_t iter;
+	isize_info_t last_ii; // this is for the last batch of reads
+	char str[1024], magic[2][4];
+	bwt_t *bwt;
+	uint8_t *pac;
+
+	// initialization
+	bwase_initialize(); // initialize g_log_n[] in bwase.c
+	pac = 0; bwt = 0;
+	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
+	bns = bns_restore(prefix);
+	srand48(bns->seed);
+	fp_sa[0] = xopen(fn_sa[0], "r");
+	fp_sa[1] = xopen(fn_sa[1], "r");
+	g_hash = kh_init(b128);
+	last_ii.avg = -1.0;
+
+	err_fread_noeof(magic[0], 1, 4, fp_sa[0]);
+	err_fread_noeof(magic[1], 1, 4, fp_sa[1]);
+	if (strncmp(magic[0], SAI_MAGIC, 4) != 0 || strncmp(magic[1], SAI_MAGIC, 4) != 0) {
+		fprintf(stderr, "[E::%s] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.\n", __func__);
+		exit(1);
+	}
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
+	ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
+	opt0 = opt;
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
+	ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
+	{ // for Illumina alignment only
+		if (popt->is_preload) {
+			strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
+			strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
+			pac = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
+			err_rewind(bns->fp_pac);
+			err_fread_noeof(pac, 1, bns->l_pac/4+1, bns->fp_pac);
+		}
+	}
+
+	// core loop
+	bwa_print_sam_hdr(bns, rg_line);
+	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
+		int cnt_chg;
+		isize_info_t ii;
+		ubyte_t *pacseq;
+
+		seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, opt.mode, opt.trim_qual);
+		tot_seqs += n_seqs;
+		t = clock();
+
+		fprintf(stderr, "[bwa_sai2sam_pe_core] convert to sequence coordinate... \n");
+		cnt_chg = bwa_cal_pac_pos_pe(bns, prefix, bwt, n_seqs, seqs, fp_sa, &ii, popt, &opt, &last_ii);
+		fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+		fprintf(stderr, "[bwa_sai2sam_pe_core] changing coordinates of %d alignments.\n", cnt_chg);
+
+		fprintf(stderr, "[bwa_sai2sam_pe_core] align unmapped mate...\n");
+		pacseq = bwa_paired_sw(bns, pac, n_seqs, seqs, popt, &ii);
+		fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+
+		fprintf(stderr, "[bwa_sai2sam_pe_core] refine gapped alignments... ");
+		for (j = 0; j < 2; ++j)
+			bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq);
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+		if (pac == 0) free(pacseq);
+
+		fprintf(stderr, "[bwa_sai2sam_pe_core] print alignments... ");
+		for (i = 0; i < n_seqs; ++i) {
+			bwa_seq_t *p[2];
+			p[0] = seqs[0] + i; p[1] = seqs[1] + i;
+			if (p[0]->bc[0] || p[1]->bc[0]) {
+				strcat(p[0]->bc, p[1]->bc);
+				strcpy(p[1]->bc, p[0]->bc);
+			}
+			bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
+			bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
+			if (strcmp(p[0]->name, p[1]->name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", p[0]->name, p[1]->name);
+		}
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+
+		for (j = 0; j < 2; ++j)
+			bwa_free_read_seq(n_seqs, seqs[j]);
+		fprintf(stderr, "[bwa_sai2sam_pe_core] %lld sequences have been processed.\n", tot_seqs);
+		last_ii = ii;
+	}
+
+	// destroy
+	bns_destroy(bns);
+	for (i = 0; i < 2; ++i) {
+		bwa_seq_close(ks[i]);
+		err_fclose(fp_sa[i]);
+	}
+	for (iter = kh_begin(g_hash); iter != kh_end(g_hash); ++iter)
+		if (kh_exist(g_hash, iter)) free(kh_val(g_hash, iter).a);
+	kh_destroy(b128, g_hash);
+	if (pac) {
+		free(pac); bwt_destroy(bwt);
+	}
+}
+
+int bwa_sai2sam_pe(int argc, char *argv[])
+{
+	int c;
+	pe_opt_t *popt;
+	char *prefix, *rg_line = 0;
+
+	popt = bwa_init_pe_opt();
+	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
+		switch (c) {
+		case 'r':
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
+			break;
+		case 'a': popt->max_isize = atoi(optarg); break;
+		case 'o': popt->max_occ = atoi(optarg); break;
+		case 's': popt->is_sw = 0; break;
+		case 'P': popt->is_preload = 1; break;
+		case 'n': popt->n_multi = atoi(optarg); break;
+		case 'N': popt->N_multi = atoi(optarg); break;
+		case 'c': popt->ap_prior = atof(optarg); break;
+		case 'f': xreopen(optarg, "w", stdout); break;
+		case 'A': popt->force_isize = 1; break;
+		default: return 1;
+		}
+	}
+
+	if (optind + 5 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>\n\n");
+		fprintf(stderr, "Options: -a INT   maximum insert size [%d]\n", popt->max_isize);
+		fprintf(stderr, "         -o INT   maximum occurrences for one end [%d]\n", popt->max_occ);
+		fprintf(stderr, "         -n INT   maximum hits to output for paired reads [%d]\n", popt->n_multi);
+		fprintf(stderr, "         -N INT   maximum hits to output for discordant pairs [%d]\n", popt->N_multi);
+		fprintf(stderr, "         -c FLOAT prior of chimeric rate (lower bound) [%.1le]\n", popt->ap_prior);
+        fprintf(stderr, "         -f FILE  sam file to output results to [stdout]\n");
+		fprintf(stderr, "         -r STR   read group header line such as `@RG\\tID:foo\\tSM:bar' [null]\n");
+		fprintf(stderr, "         -P       preload index into memory (for base-space reads only)\n");
+		fprintf(stderr, "         -s       disable Smith-Waterman for the unmapped mate\n");
+		fprintf(stderr, "         -A       disable insert size estimate (force -s)\n\n");
+		fprintf(stderr, "Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
+		fprintf(stderr, "       2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
+		fprintf(stderr, "          to get a sensible speed at the cost of pairing accuracy.\n");
+		fprintf(stderr, "\n");
+		return 1;
+	}
+	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+		return 1;
+	}
+	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
+	free(prefix); free(popt);
+	return 0;
+}

bwase.c

@@ -0,0 +1,606 @@
+#include <unistd.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <assert.h>
+#include "bwase.h"
+#include "bwtaln.h"
+#include "bntseq.h"
+#include "utils.h"
+#include "kstring.h"
+#include "bwa.h"
+#include "ksw.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+int g_log_n[256];
+
+void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
+{
+	int i, cnt, best;
+	if (n_aln == 0) {
+		s->type = BWA_TYPE_NO_MATCH;
+		s->c1 = s->c2 = 0;
+		return;
+	}
+
+	if (set_main) {
+		best = aln[0].score;
+		for (i = cnt = 0; i < n_aln; ++i) {
+			const bwt_aln1_t *p = aln + i;
+			if (p->score > best) break;
+			if (drand48() * (p->l - p->k + 1 + cnt) > (double)cnt) {
+				s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape;
+				s->ref_shift = (int)p->n_del - (int)p->n_ins;
+				s->score = p->score;
+				s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
+			}
+			cnt += p->l - p->k + 1;
+		}
+		s->c1 = cnt;
+		for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
+		s->c2 = cnt - s->c1;
+		s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
+	}
+
+	if (n_multi) {
+		int k, rest, n_occ, z = 0;
+		for (k = n_occ = 0; k < n_aln; ++k) {
+			const bwt_aln1_t *q = aln + k;
+			n_occ += q->l - q->k + 1;
+		}
+		if (s->multi) free(s->multi);
+		if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
+			s->multi = 0; s->n_multi = 0;
+			return;
+		}
+		/* The following code is more flexible than what is required
+		 * here. In principle, due to the requirement above, we can
+		 * simply output all hits, but the following samples "rest"
+		 * number of random hits. */
+		rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
+		s->multi = calloc(rest, sizeof(bwt_multi1_t));
+		for (k = 0; k < n_aln; ++k) {
+			const bwt_aln1_t *q = aln + k;
+			if (q->l - q->k + 1 <= rest) {
+				bwtint_t l;
+				for (l = q->k; l <= q->l; ++l) {
+					s->multi[z].pos = l;
+					s->multi[z].gap = q->n_gapo + q->n_gape;
+					s->multi[z].ref_shift = (int)q->n_del - (int)q->n_ins;
+					s->multi[z++].mm = q->n_mm;
+				}
+				rest -= q->l - q->k + 1;
+			} else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here. 
+				int j, i;
+				for (j = rest, i = q->l - q->k + 1; j > 0; --j) {
+					double p = 1.0, x = drand48();
+					while (x < p) p -= p * j / (i--);
+					s->multi[z].pos = q->l - i;
+					s->multi[z].gap = q->n_gapo + q->n_gape;
+					s->multi[z].ref_shift = (int)q->n_del - (int)q->n_ins;
+					s->multi[z++].mm = q->n_mm;
+				}
+				rest = 0;
+				break;
+			}
+		}
+		s->n_multi = z;
+	}
+}
+
+void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
+{
+	bwa_aln2seq_core(n_aln, aln, s, 1, 0);
+}
+
+int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
+{
+	int n;
+	if (p->c1 == 0) return 23;
+	if (p->c1 > 1) return 0;
+	if (p->n_mm == mm) return 25;
+	if (p->c2 == 0) return 37;
+	n = (p->c2 >= 255)? 255 : p->c2;
+	return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
+}
+
+bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int ref_len, int *strand)
+{
+	bwtint_t pos_f;
+	int is_rev;
+	*strand = 0; // initialise strand to 0 otherwise we could return without setting it
+	pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
+	if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
+	pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base
+	*strand = !is_rev;
+	if (is_rev) pos_f = pos_f + 1 < ref_len? 0 : pos_f - ref_len + 1; // position of the first base
+	return pos_f; // FIXME: it is possible that pos_f < bns->anns[ref_id].offset
+}
+
+/**
+ * Derive the actual position in the read from the given suffix array
+ * coordinates. Note that the position will be approximate based on
+ * whether indels appear in the read and whether calculations are
+ * performed from the start or end of the read.
+ */
+void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t *bwt, bwa_seq_t *seq, const int max_mm, const float fnr)
+{
+	int max_diff, strand;
+	if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) return;
+	max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
+	seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
+	//fprintf(stderr, "%d\n", seq->ref_shift);
+	seq->pos = bwa_sa2pos(bns, bwt, seq->sa, seq->len + seq->ref_shift, &strand);
+	seq->strand = strand;
+	seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
+	if (seq->pos == (bwtint_t)-1) seq->type = BWA_TYPE_NO_MATCH;
+}
+
+void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
+{
+	int i, j, strand, n_multi;
+	char str[1024];
+	bwt_t *bwt;
+	// load forward SA
+	strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
+	strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p = &seqs[i];
+		bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
+		for (j = n_multi = 0; j < p->n_multi; ++j) {
+			bwt_multi1_t *q = p->multi + j;
+			q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + q->ref_shift, &strand);
+			q->strand = strand;
+			if (q->pos != p->pos && q->pos != (bwtint_t)-1)
+				p->multi[n_multi++] = *q;
+		}
+		p->n_multi = n_multi;
+	}
+	bwt_destroy(bwt);
+}
+
+#define SW_BW 50
+
+bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, ubyte_t *seq, int ref_shift, bwtint_t *_rb, int *n_cigar)
+{
+	bwa_cigar_t *cigar = 0;
+	uint32_t *cigar32 = 0;
+	ubyte_t *rseq;
+	int64_t k, rb, re, rlen;
+	int8_t mat[25];
+	int w;
+
+	bwa_fill_scmat(1, 3, mat);
+	rb = *_rb; re = rb + len + ref_shift;
+	assert(re <= l_pac);
+	rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
+	assert(re - rb == rlen);
+	w = abs((int)rlen - len) * 1.5;
+	ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > w? SW_BW : w, n_cigar, &cigar32);
+	assert(*n_cigar > 0);
+	if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; // change endding ins to soft clipping
+	if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 3; // change beginning ins to soft clipping
+	if ((cigar32[*n_cigar - 1]&0xf) == 2) --*n_cigar; // delete endding del
+	if ((cigar32[0]&0xf) == 2) { // delete beginning del
+		*_rb += cigar32[0]>>4;
+		--*n_cigar;
+		memmove(cigar32, cigar32+1, (*n_cigar) * 4);
+	}
+	cigar = (bwa_cigar_t*)cigar32;
+	for (k = 0; k < *n_cigar; ++k)
+		cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
+	free(rseq);
+	return cigar;
+}
+
+char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
+				  bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
+{
+	bwtint_t x, y;
+	int z, u, c, nm = 0;
+	str->l = 0; // reset
+	x = pos; y = 0;
+	if (cigar) {
+		int k, l;
+		for (k = u = 0; k < n_cigar; ++k) {
+			l = __cigar_len(cigar[k]);
+			if (__cigar_op(cigar[k]) == FROM_M) {
+				for (z = 0; z < l && x+z < l_pac; ++z) {
+					c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
+					if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
+						ksprintf(str, "%d", u);
+						kputc("ACGTN"[c], str);
+						++nm;
+						u = 0;
+					} else ++u;
+				}
+				x += l; y += l;
+			} else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
+				y += l;
+				if (__cigar_op(cigar[k]) == FROM_I) nm += l;
+			} else if (__cigar_op(cigar[k]) == FROM_D) {
+				ksprintf(str, "%d", u);
+				kputc('^', str);
+				for (z = 0; z < l && x+z < l_pac; ++z)
+					kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
+				u = 0;
+				x += l; nm += l;
+			}
+		}
+	} else { // no gaps
+		for (z = u = 0; z < (bwtint_t)len && x+z < l_pac; ++z) {
+			c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
+			if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
+				ksprintf(str, "%d", u);
+				kputc("ACGTN"[c], str);
+				++nm;
+				u = 0;
+			} else ++u;
+		}
+	}
+	ksprintf(str, "%d", u);
+	*_nm = nm;
+	return strdup(str->s);
+}
+
+void bwa_correct_trimmed(bwa_seq_t *s)
+{
+	if (s->len == s->full_len) return;
+	if (s->strand == 0) { // forward
+		if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
+			s->cigar[s->n_cigar-1] += s->full_len - s->len;
+		} else {
+			if (s->cigar == 0) {
+				s->n_cigar = 2;
+				s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
+				s->cigar[0] = __cigar_create(0, s->len);
+			} else {
+				++s->n_cigar;
+				s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
+			}
+			s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
+		}
+	} else { // reverse
+		if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
+			s->cigar[0] += s->full_len - s->len;
+		} else {
+			if (s->cigar == 0) {
+				s->n_cigar = 2;
+				s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
+				s->cigar[1] = __cigar_create(0, s->len);
+			} else {
+				++s->n_cigar;
+				s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
+				memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
+			}
+			s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
+		}
+	}
+	s->len = s->full_len;
+}
+
+void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq)
+{
+	ubyte_t *pacseq;
+	int i, j, k;
+	kstring_t *str;
+
+	if (!_pacseq) {
+		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
+		err_rewind(bns->fp_pac);
+		err_fread_noeof(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
+	} else pacseq = _pacseq;
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *s = seqs + i;
+		seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
+		for (j = k = 0; j < s->n_multi; ++j) {
+			bwt_multi1_t *q = s->multi + j;
+			int n_cigar;
+			if (q->gap) { // gapped alignment
+				q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, q->ref_shift, &q->pos, &n_cigar);
+				q->n_cigar = n_cigar;
+				if (q->cigar) s->multi[k++] = *q;
+			} else s->multi[k++] = *q;
+		}
+		s->n_multi = k; // this squeezes out gapped alignments which failed the CIGAR generation
+		if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
+		s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, s->ref_shift, &s->pos, &s->n_cigar);
+		if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
+	}
+	// generate MD tag
+	str = (kstring_t*)calloc(1, sizeof(kstring_t));
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *s = seqs + i;
+		if (s->type != BWA_TYPE_NO_MATCH) {
+			int nm;
+			s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq, bns->l_pac, pacseq, str, &nm);
+			s->nm = nm;
+		}
+	}
+	free(str->s); free(str);
+
+	// correct for trimmed reads
+	for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
+
+	if (!_pacseq) free(pacseq);
+}
+
+int64_t pos_end(const bwa_seq_t *p)
+{
+	if (p->cigar) {
+		int j;
+		int64_t x = p->pos;
+		for (j = 0; j != p->n_cigar; ++j) {
+			int op = __cigar_op(p->cigar[j]);
+			if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
+		}
+		return x;
+	} else return p->pos + p->len;
+}
+
+int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
+{
+	if (p->cigar) {
+		int j;
+		int64_t x = p->pos;
+		for (j = 0; j != p->n_cigar; ++j) {
+			int op = __cigar_op(p->cigar[j]);
+			if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
+		}
+		return x;
+	} else return p->pos + len;
+}
+
+static int64_t pos_5(const bwa_seq_t *p)
+{
+	if (p->type != BWA_TYPE_NO_MATCH)
+		return p->strand? pos_end(p) : p->pos;
+	return -1;
+}
+
+void bwa_print_seq(FILE *stream, bwa_seq_t *seq) {
+	char buffer[4096];
+	const int bsz = sizeof(buffer);
+	int i, j, l;
+	
+	if (seq->strand == 0) {
+		for (i = 0; i < seq->full_len; i += bsz) {
+			l = seq->full_len - i > bsz ? bsz : seq->full_len - i;
+			for (j = 0; j < l; j++) buffer[j] = "ACGTN"[seq->seq[i + j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	} else {
+		for (i = seq->full_len - 1; i >= 0; i -= bsz) {
+			l = i + 1 > bsz ? bsz : i + 1;
+			for (j = 0; j < l; j++) buffer[j] = "TGCAN"[seq->seq[i - j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	}
+}
+
+void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
+{
+	int j;
+	if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
+		int seqid, nn, am = 0, flag = p->extra_flag;
+		char XT;
+
+		if (p->type == BWA_TYPE_NO_MATCH) {
+			p->pos = mate->pos;
+			p->strand = mate->strand;
+			flag |= SAM_FSU;
+			j = 1;
+		} else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
+
+		// get seqid
+		nn = bns_cnt_ambi(bns, p->pos, j, &seqid);
+		if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
+			flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
+
+		// update flag and print it
+		if (p->strand) flag |= SAM_FSR;
+		if (mate) {
+			if (mate->type != BWA_TYPE_NO_MATCH) {
+				if (mate->strand) flag |= SAM_FMR;
+			} else flag |= SAM_FMU;
+		}
+		err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
+		err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
+
+		// print CIGAR
+		if (p->cigar) {
+			for (j = 0; j != p->n_cigar; ++j)
+				err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
+		} else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
+		else err_printf("%dM", p->len);
+
+		// print mate coordinate
+		if (mate && mate->type != BWA_TYPE_NO_MATCH) {
+			int m_seqid;
+			long long isize;
+			am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
+			// redundant calculation here, but should not matter too much
+			bns_cnt_ambi(bns, mate->pos, mate->len, &m_seqid);
+			err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
+			isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
+			if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
+			err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
+		} else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
+		else err_printf("\t*\t0\t0\t");
+
+		// print sequence and quality
+		bwa_print_seq(stdout, p);
+		err_putchar('\t');
+		if (p->qual) {
+			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
+			err_printf("%s", p->qual);
+		} else err_printf("*");
+
+		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
+		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
+		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
+		if (p->type != BWA_TYPE_NO_MATCH) {
+			int i;
+			// calculate XT tag
+			XT = "NURM"[p->type];
+			if (nn > 10) XT = 'N';
+			// print tags
+			err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
+			if (nn) err_printf("\tXN:i:%d", nn);
+			if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
+			if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
+				err_printf("\tX0:i:%d", p->c1);
+				if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
+			}
+			err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
+			if (p->md) err_printf("\tMD:Z:%s", p->md);
+			// print multiple hits
+			if (p->n_multi) {
+				err_printf("\tXA:Z:");
+				for (i = 0; i < p->n_multi; ++i) {
+					bwt_multi1_t *q = p->multi + i;
+					int k;
+					j = pos_end_multi(q, p->len) - q->pos;
+					nn = bns_cnt_ambi(bns, q->pos, j, &seqid);
+					err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
+						   (int)(q->pos - bns->anns[seqid].offset + 1));
+					if (q->cigar) {
+						for (k = 0; k < q->n_cigar; ++k)
+							err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
+					} else err_printf("%dM", p->len);
+					err_printf(",%d;", q->gap + q->mm);
+				}
+			}
+		}
+		err_putchar('\n');
+	} else { // this read has no match
+		//ubyte_t *s = p->strand? p->rseq : p->seq;
+		int flag = p->extra_flag | SAM_FSU;
+		if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
+		err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
+		//Why did this work differently to the version above??
+		//for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
+		bwa_print_seq(stdout, p);
+		err_putchar('\t');
+		if (p->qual) {
+			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
+			err_printf("%s", p->qual);
+		} else err_printf("*");
+		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
+		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
+		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
+		err_putchar('\n');
+	}
+}
+
+void bwase_initialize() 
+{
+	int i;
+	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
+}
+
+void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
+{
+	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
+	int i, n_seqs, m_aln;
+	long long tot_seqs = 0;
+	bwt_aln1_t *aln = 0;
+	bwa_seq_t *seqs;
+	bwa_seqio_t *ks;
+	clock_t t;
+	bntseq_t *bns;
+	FILE *fp_sa;
+	gap_opt_t opt;
+	char magic[4];
+
+	// initialization
+	bwase_initialize();
+	bns = bns_restore(prefix);
+	srand48(bns->seed);
+	fp_sa = xopen(fn_sa, "r");
+
+	m_aln = 0;
+	err_fread_noeof(magic, 1, 4, fp_sa);
+	if (strncmp(magic, SAI_MAGIC, 4) != 0) {
+		fprintf(stderr, "[E::%s] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.\n", __func__);
+		exit(1);
+	}
+	err_fread_noeof(&opt, sizeof(gap_opt_t), 1, fp_sa);
+	bwa_print_sam_hdr(bns, rg_line);
+	// set ks
+	ks = bwa_open_reads(opt.mode, fn_fa);
+	// core loop
+	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode, opt.trim_qual)) != 0) {
+		tot_seqs += n_seqs;
+		t = clock();
+
+		// read alignment
+		for (i = 0; i < n_seqs; ++i) {
+			bwa_seq_t *p = seqs + i;
+			int n_aln;
+			err_fread_noeof(&n_aln, 4, 1, fp_sa);
+			if (n_aln > m_aln) {
+				m_aln = n_aln;
+				aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
+			}
+			err_fread_noeof(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
+			bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
+		}
+
+		fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
+		bwa_cal_pac_pos(bns, prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+
+		fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
+		bwa_refine_gapped(bns, n_seqs, seqs, 0);
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
+
+		fprintf(stderr, "[bwa_aln_core] print alignments... ");
+		for (i = 0; i < n_seqs; ++i)
+			bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+
+		bwa_free_read_seq(n_seqs, seqs);
+		fprintf(stderr, "[bwa_aln_core] %lld sequences have been processed.\n", tot_seqs);
+	}
+
+	// destroy
+	bwa_seq_close(ks);
+	bns_destroy(bns);
+	err_fclose(fp_sa);
+	free(aln);
+}
+
+int bwa_sai2sam_se(int argc, char *argv[])
+{
+	int c, n_occ = 3;
+	char *prefix, *rg_line = 0;
+	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
+		switch (c) {
+		case 'h': break;
+		case 'r':
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
+			break;
+		case 'n': n_occ = atoi(optarg); break;
+		case 'f': xreopen(optarg, "w", stdout); break;
+		default: return 1;
+		}
+	}
+
+	if (optind + 3 > argc) {
+		fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
+		return 1;
+	}
+	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+		return 1;
+	}
+	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
+	free(prefix);
+	return 0;
+}

bwase.h

@@ -0,0 +1,29 @@
+#ifndef BWASE_H
+#define BWASE_H
+
+#include "bntseq.h"
+#include "bwt.h"
+#include "bwtaln.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	// Initialize mapping tables in the bwa single-end mapper.
+	void bwase_initialize();
+	// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
+	void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
+	// Refine the approximate position of the sequence to an actual placement for the sequence.
+	void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq);
+	// Backfill certain alignment properties mainly centering around number of matches.
+	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
+	// Calculate the end position of a read given a certain sequence.
+	int64_t pos_end(const bwa_seq_t *p);
+	//
+	bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif // BWASE_H

bwaseqio.c

@@ -0,0 +1,235 @@
+#include <zlib.h>
+#include <ctype.h>
+#include "bwtaln.h"
+#include "utils.h"
+#include "bamlite.h"
+
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+extern unsigned char nst_nt4_table[256];
+static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+struct __bwa_seqio_t {
+	// for BAM input
+	int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
+	bamFile fp;
+	// for fastq input
+	kseq_t *ks;
+};
+
+bwa_seqio_t *bwa_bam_open(const char *fn, int which)
+{
+	bwa_seqio_t *bs;
+	bam_header_t *h;
+	bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
+	bs->is_bam = 1;
+	bs->which = which;
+	bs->fp = bam_open(fn, "r");
+	if (0 == bs->fp) err_fatal_simple("Couldn't open bam file");
+	h = bam_header_read(bs->fp);
+	bam_header_destroy(h);
+	return bs;
+}
+
+bwa_seqio_t *bwa_seq_open(const char *fn)
+{
+	gzFile fp;
+	bwa_seqio_t *bs;
+	bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
+	fp = xzopen(fn, "r");
+	bs->ks = kseq_init(fp);
+	return bs;
+}
+
+void bwa_seq_close(bwa_seqio_t *bs)
+{
+	if (bs == 0) return;
+	if (bs->is_bam) {
+		if (0 != bam_close(bs->fp)) err_fatal_simple("Error closing bam file");
+	} else {
+		err_gzclose(bs->ks->f->f);
+		kseq_destroy(bs->ks);
+	}
+	free(bs);
+}
+
+void seq_reverse(int len, ubyte_t *seq, int is_comp)
+{
+	int i;
+	if (is_comp) {
+		for (i = 0; i < len>>1; ++i) {
+			char tmp = seq[len-1-i];
+			if (tmp < 4) tmp = 3 - tmp;
+			seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
+			seq[i] = tmp;
+		}
+		if (len&1) seq[i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
+	} else {
+		for (i = 0; i < len>>1; ++i) {
+			char tmp = seq[len-1-i];
+			seq[len-1-i] = seq[i]; seq[i] = tmp;
+		}
+	}
+}
+
+int bwa_trim_read(int trim_qual, bwa_seq_t *p)
+{
+	int s = 0, l, max = 0, max_l = p->len;
+	if (trim_qual < 1 || p->qual == 0) return 0;
+	for (l = p->len - 1; l >= BWA_MIN_RDLEN; --l) {
+		s += trim_qual - (p->qual[l] - 33);
+		if (s < 0) break;
+		if (s > max) max = s, max_l = l;
+	}
+	p->clip_len = p->len = max_l;
+	return p->full_len - p->len;
+}
+
+static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
+{
+	bwa_seq_t *seqs, *p;
+	int n_seqs, l, i;
+	long n_trimmed = 0, n_tot = 0;
+	bam1_t *b;
+	int res;
+
+	b = bam_init1();
+	n_seqs = 0;
+	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
+	while ((res = bam_read1(bs->fp, b)) >= 0) {
+		uint8_t *s, *q;
+		int go = 0;
+		if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
+		if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
+		if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
+		if (go == 0) continue;
+		l = b->core.l_qseq;
+		p = &seqs[n_seqs++];
+		p->tid = -1; // no assigned to a thread
+		p->qual = 0;
+		p->full_len = p->clip_len = p->len = l;
+		n_tot += p->full_len;
+		s = bam1_seq(b); q = bam1_qual(b);
+		p->seq = (ubyte_t*)calloc(p->len + 1, 1);
+		p->qual = (ubyte_t*)calloc(p->len + 1, 1);
+		for (i = 0; i != p->full_len; ++i) {
+			p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
+			p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
+		}
+		if (bam1_strand(b)) { // then reverse 
+			seq_reverse(p->len, p->seq, 1);
+			seq_reverse(p->len, p->qual, 0);
+		}
+		if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
+		p->rseq = (ubyte_t*)calloc(p->full_len, 1);
+		memcpy(p->rseq, p->seq, p->len);
+		seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
+		seq_reverse(p->len, p->rseq, is_comp);
+		p->name = strdup((const char*)bam1_qname(b));
+		if (n_seqs == n_needed) break;
+	}
+	if (res < 0 && res != -1) err_fatal_simple("Error reading bam file");
+	*n = n_seqs;
+	if (n_seqs && trim_qual >= 1)
+		fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
+	if (n_seqs == 0) {
+		free(seqs);
+		bam_destroy1(b);
+		return 0;
+	}
+	bam_destroy1(b);
+	return seqs;
+}
+
+#define BARCODE_LOW_QUAL 13
+
+bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
+{
+	bwa_seq_t *seqs, *p;
+	kseq_t *seq = bs->ks;
+	int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
+	long n_trimmed = 0, n_tot = 0;
+
+	if (l_bc > BWA_MAX_BCLEN) {
+		fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
+		return 0;
+	}
+	if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
+	n_seqs = 0;
+	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
+	while ((l = kseq_read(seq)) >= 0) {
+		if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
+			// skip reads that are marked to be filtered by Casava
+			char *s = index(seq->comment.s, ':');
+			if (s && *(++s) == 'Y') {
+				continue;
+			}
+		}
+		if (is_64 && seq->qual.l)
+			for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
+		if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
+		p = &seqs[n_seqs++];
+		if (l_bc) { // then trim barcode
+			for (i = 0; i < l_bc; ++i)
+				p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
+			p->bc[i] = 0;
+			for (; i < seq->seq.l; ++i)
+				seq->seq.s[i - l_bc] = seq->seq.s[i];
+			seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
+			if (seq->qual.l) {
+				for (i = l_bc; i < seq->qual.l; ++i)
+					seq->qual.s[i - l_bc] = seq->qual.s[i];
+				seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
+			}
+			l = seq->seq.l;
+		} else p->bc[0] = 0;
+		p->tid = -1; // no assigned to a thread
+		p->qual = 0;
+		p->full_len = p->clip_len = p->len = l;
+		n_tot += p->full_len;
+		p->seq = (ubyte_t*)calloc(p->full_len, 1);
+		for (i = 0; i != p->full_len; ++i)
+			p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
+		if (seq->qual.l) { // copy quality
+			p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
+			if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
+		}
+		p->rseq = (ubyte_t*)calloc(p->full_len, 1);
+		memcpy(p->rseq, p->seq, p->len);
+		seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
+		seq_reverse(p->len, p->rseq, is_comp);
+		p->name = strdup((const char*)seq->name.s);
+		{ // trim /[12]$
+			int t = strlen(p->name);
+			if (t > 2 && p->name[t-2] == '/' && (p->name[t-1] == '1' || p->name[t-1] == '2')) p->name[t-2] = '\0';
+		}
+		if (n_seqs == n_needed) break;
+	}
+	*n = n_seqs;
+	if (n_seqs && trim_qual >= 1)
+		fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
+	if (n_seqs == 0) {
+		free(seqs);
+		return 0;
+	}
+	return seqs;
+}
+
+void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
+{
+	int i, j;
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p = seqs + i;
+		for (j = 0; j < p->n_multi; ++j)
+			if (p->multi[j].cigar) free(p->multi[j].cigar);
+		free(p->name);
+		free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
+		free(p->cigar);
+	}
+	free(seqs);
+}

bwashm.c

@@ -0,0 +1,213 @@
+#include <sys/types.h>
+#include <sys/mman.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <errno.h>
+#include <stdio.h>
+#include "bwa.h"
+
+int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
+{
+	const char *name;
+	uint8_t *shm, *shm_idx;
+	uint16_t *cnt;
+	int shmid, to_init = 0, l;
+	char path[PATH_MAX + 1], *tmpfn = (char*)_tmpfn;
+
+	if (hint == 0 || hint[0] == 0) return -1;
+	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
+	++name;
+
+	if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
+		shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
+		to_init = 1;
+	}
+	if (shmid < 0) return -1;
+	ftruncate(shmid, BWA_CTL_SIZE);
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	if (to_init) {
+		memset(shm, 0, BWA_CTL_SIZE);
+		cnt[1] = 4;
+	}
+
+	if (idx->mem == 0) bwa_idx2mem(idx);
+
+	if (tmpfn) {
+		FILE *fp;
+		if ((fp = fopen(tmpfn, "wb")) != 0) {
+			int64_t rest = idx->l_mem;
+			while (rest > 0) {
+				int64_t l = rest < 0x1000000? rest : 0x1000000;
+				rest -= fwrite(&idx->mem[idx->l_mem - rest], 1, l, fp);
+			}
+			fclose(fp);
+			free(idx->mem); idx->mem = 0;
+		} else {
+			fprintf(stderr, "[W::%s] fail to create the temporary file. Option '-f' is ignored.\n", __func__);
+			tmpfn = 0;
+		}
+	}
+
+	strcat(strcpy(path, "/bwaidx-"), name);
+	if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
+		shm_unlink(path);
+		perror("shm_open()");
+		return -1;
+	}
+	l = 8 + strlen(name) + 1;
+	if (cnt[1] + l > BWA_CTL_SIZE) return -1;
+	memcpy(shm + cnt[1], &idx->l_mem, 8);
+	memcpy(shm + cnt[1] + 8, name, l - 8);
+	cnt[1] += l; ++cnt[0];
+	ftruncate(shmid, idx->l_mem);
+	shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
+	if (tmpfn) {
+		FILE *fp;
+		fp = fopen(tmpfn, "rb");
+		int64_t rest = idx->l_mem;
+		while (rest > 0) {
+			int64_t l = rest < 0x1000000? rest : 0x1000000;
+			rest -= fread(&shm_idx[idx->l_mem - rest], 1, l, fp);
+		}
+		fclose(fp);
+		unlink(tmpfn);
+	} else {
+		memcpy(shm_idx, idx->mem, idx->l_mem);
+		free(idx->mem);
+	}
+	bwa_mem2idx(idx->l_mem, shm_idx, idx);
+	idx->is_shm = 1;
+	return 0;
+}
+
+bwaidx_t *bwa_idx_load_from_shm(const char *hint)
+{
+	const char *name;
+	uint8_t *shm, *shm_idx;
+	uint16_t *cnt, i;
+	char *p, path[PATH_MAX + 1];
+	int shmid;
+	int64_t l_mem;
+	bwaidx_t *idx;
+
+	if (hint == 0 || hint[0] == 0) return 0;
+	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
+	++name;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	if (cnt[0] == 0) return 0;
+	for (i = 0, p = (char*)(shm + 4); i < cnt[0]; ++i) {
+		memcpy(&l_mem, p, 8); p += 8;
+		if (strcmp(p, name) == 0) break;
+		p += strlen(p) + 1;
+	}
+	if (i == cnt[0]) return 0;
+
+	strcat(strcpy(path, "/bwaidx-"), name);
+	if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0;
+	shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0);
+	idx = calloc(1, sizeof(bwaidx_t));
+	bwa_mem2idx(l_mem, shm_idx, idx);
+	idx->is_shm = 1;
+	return idx;
+}
+
+int bwa_shm_test(const char *hint)
+{
+	int shmid;
+	uint16_t *cnt, i;
+	char *p, *shm;
+	const char *name;
+
+	if (hint == 0 || hint[0] == 0) return 0;
+	for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
+	++name;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
+		if (strcmp(p + 8, name) == 0) return 1;
+		p += strlen(p) + 9;
+	}
+	return 0;
+}
+
+int bwa_shm_list(void)
+{
+	int shmid;
+	uint16_t *cnt, i;
+	char *p, *shm;
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
+		int64_t l_mem;
+		memcpy(&l_mem, p, 8); p += 8;
+		printf("%s\t%ld\n", p, (long)l_mem);
+		p += strlen(p) + 1;
+	}
+	return 0;
+}
+
+int bwa_shm_destroy(void)
+{
+	int shmid;
+	uint16_t *cnt, i;
+	char *p, *shm;
+	char path[PATH_MAX + 1];
+
+	if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
+	shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
+	cnt = (uint16_t*)shm;
+	for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
+		int64_t l_mem;
+		memcpy(&l_mem, p, 8); p += 8;
+		strcat(strcpy(path, "/bwaidx-"), p);
+		shm_unlink(path);
+		p += strlen(p) + 1;
+	}
+	munmap(shm, BWA_CTL_SIZE);
+	shm_unlink("/bwactl");
+	return 0;
+}
+
+int main_shm(int argc, char *argv[])
+{
+	int c, to_list = 0, to_drop = 0, ret = 0;
+	char *tmpfn = 0;
+	while ((c = getopt(argc, argv, "ldf:")) >= 0) {
+		if (c == 'l') to_list = 1;
+		else if (c == 'd') to_drop = 1;
+		else if (c == 'f') tmpfn = optarg;
+	}
+	if (optind == argc && !to_list && !to_drop) {
+		fprintf(stderr, "\nUsage: bwa shm [-d|-l] [-f tmpFile] [idxbase]\n\n");
+		fprintf(stderr, "Options: -d       destroy all indices in shared memory\n");
+		fprintf(stderr, "         -l       list names of indices in shared memory\n");
+		fprintf(stderr, "         -f FILE  temporary file to reduce peak memory\n\n");
+		return 1;
+	}
+	if (optind < argc && (to_list || to_drop)) {
+		fprintf(stderr, "[E::%s] open -l or -d cannot be used when 'idxbase' is present\n", __func__);
+		return 1;
+	}
+	if (optind < argc) {
+		if (bwa_shm_test(argv[optind]) == 0) {
+			bwaidx_t *idx;
+			idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
+			if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) {
+				fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
+				ret = 1;
+			}
+			bwa_idx_destroy(idx);
+		} else fprintf(stderr, "[M::%s] index '%s' is already in shared memory\n", __func__, argv[optind]);
+	}
+	if (to_list) bwa_shm_list();
+	if (to_drop) bwa_shm_destroy();
+	return ret;
+}

bwt.c

@@ -0,0 +1,477 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3@sanger.ac.uk> */
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <stdint.h>
+#include <limits.h>
+#include "utils.h"
+#include "bwt.h"
+#include "kvec.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+// 计算一个字节构成的A,T,C,G序列，对应的每个碱基的个数，因为最多有4个相同的碱基，所以每次左移3位就行
+void bwt_gen_cnt_table(bwt_t *bwt)
+{
+	int i, j;
+	for (i = 0; i != 256; ++i) {
+		uint32_t x = 0;
+		for (j = 0; j != 4; ++j)
+			x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
+		bwt->cnt_table[i] = x;
+	}
+}
+
+static inline bwtint_t bwt_invPsi(const bwt_t *bwt, bwtint_t k) // compute inverse CSA
+{
+	bwtint_t x = k - (k > bwt->primary); // bwt中不包含$，所以位置超过序列长度后，要减掉1，（因为后边加上了互补链）
+	// x = bwt_B0(bwt, x); // 获取x位置对应的字符
+
+	uint32_t t1 = (bwt->bwt[((x) >> 7 << 4) + sizeof(bwtint_t) + (((x) & 0x7f) >> 4)]);
+	uint32_t t2 = t1 >> ((~(x) & 0xf) << 1) & 3;
+
+	x = t2;
+
+	x = bwt->L2[x] + bwt_occ(bwt, k, x); // 获取x字符在k位置（后缀索引），
+	return k == bwt->primary? 0 : x;
+}
+
+// bwt->bwt and bwt->occ must be precalculated
+void bwt_cal_sa(bwt_t *bwt, int intv)
+{
+	bwtint_t isa, sa, i; // S(isa) = sa isa是后缀数组的索引，sa表示位置
+	int intv_round = intv; // 间隔多少来保存一个位置信息
+
+	kv_roundup32(intv_round);
+	xassert(intv_round == intv, "SA sample interval is not a power of 2.");
+	xassert(bwt->bwt, "bwt_t::bwt is not initialized.");
+
+	if (bwt->sa) free(bwt->sa);
+	bwt->sa_intv = intv;
+	bwt->n_sa = (bwt->seq_len + intv) / intv;
+	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t)); // 用64位无符号整数来保存位置信息，其实用33位就够了
+	// calculate SA value
+	isa = 0; sa = bwt->seq_len;
+	for (i = 0; i < bwt->seq_len; ++i) {
+		if (isa % intv == 0) bwt->sa[isa/intv] = sa; // 第一个位置是$，所以位置就是序列长度
+		--sa; // 从后往前，一个位置一个位置的找对应的后缀数组，isa就是与sa对应的后缀数组排序后在sa数组中的相对位置
+		isa = bwt_invPsi(bwt, isa); // 下一个后缀数组的相对位置
+	}
+	if (isa % intv == 0) bwt->sa[isa/intv] = sa;
+	bwt->sa[0] = (bwtint_t)-1; // before this line, bwt->sa[0] = bwt->seq_len
+}
+
+bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
+{
+	bwtint_t sa = 0, mask = bwt->sa_intv - 1;
+	while (k & mask) {
+		++sa;
+		k = bwt_invPsi(bwt, k);
+	}
+	/* without setting bwt->sa[0] = -1, the following line should be
+	   changed to (sa + bwt->sa[k/bwt->sa_intv]) % (bwt->seq_len + 1) */
+	return sa + bwt->sa[k/bwt->sa_intv];
+}
+
+static inline int __occ_aux(uint64_t y, int c)
+{
+	// reduce nucleotide counting to bits counting
+	y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
+	// count the number of 1s in y
+	y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
+	return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
+}
+
+bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
+{
+	bwtint_t n;
+	uint32_t *p, *end;
+
+	if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
+	if (k == (bwtint_t)(-1)) return 0;
+	k -= (k >= bwt->primary); // because $ is not in bwt
+
+	// retrieve Occ at k/OCC_INTERVAL
+	n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
+	p += sizeof(bwtint_t); // jump to the start of the first BWT cell
+
+	// calculate Occ up to the last k/32
+	end = p + (((k>>5) - ((k&~OCC_INTV_MASK)>>5))<<1);
+	for (; p < end; p += 2) n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
+
+	// calculate Occ
+	n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
+	if (c == 0) n -= ~k&31; // corrected for the masked bits
+
+	return n;
+}
+
+// an analogy to bwt_occ() but more efficient, requiring k <= l
+void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
+{
+	bwtint_t _k, _l;
+	_k = (k >= bwt->primary)? k-1 : k;
+	_l = (l >= bwt->primary)? l-1 : l;
+	if (_l/OCC_INTERVAL != _k/OCC_INTERVAL || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
+		*ok = bwt_occ(bwt, k, c);
+		*ol = bwt_occ(bwt, l, c);
+	} else {
+		bwtint_t m, n, i, j;
+		uint32_t *p;
+		if (k >= bwt->primary) --k;
+		if (l >= bwt->primary) --l;
+		n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
+		p += sizeof(bwtint_t);
+		// calculate *ok
+		j = k >> 5 << 5;
+		for (i = k/OCC_INTERVAL*OCC_INTERVAL; i < j; i += 32, p += 2)
+			n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
+		m = n;
+		n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
+		if (c == 0) n -= ~k&31; // corrected for the masked bits
+		*ok = n;
+		// calculate *ol
+		j = l >> 5 << 5;
+		for (; i < j; i += 32, p += 2)
+			m += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
+		m += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~l&31)<<1)) - 1), c);
+		if (c == 0) m -= ~l&31; // corrected for the masked bits
+		*ol = m;
+	}
+}
+
+#define __occ_aux4(bwt, b)											\
+	((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff]		\
+	 + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])
+
+void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
+{
+	bwtint_t x;
+	uint32_t *p, tmp, *end;
+	if (k == (bwtint_t)(-1)) {
+		memset(cnt, 0, 4 * sizeof(bwtint_t));
+		return;
+	}
+	k -= (k >= bwt->primary); // because $ is not in bwt
+	p = bwt_occ_intv(bwt, k);
+	memcpy(cnt, p, 4 * sizeof(bwtint_t));
+	p += sizeof(bwtint_t); // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
+	end = p + ((k>>4) - ((k&~OCC_INTV_MASK)>>4)); // this is the end point of the following loop
+	for (x = 0; p < end; ++p) x += __occ_aux4(bwt, *p);
+	tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
+	x += __occ_aux4(bwt, tmp) - (~k&15);
+	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
+}
+
+// an analogy to bwt_occ4() but more efficient, requiring k <= l
+void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
+{
+	bwtint_t _k, _l;
+	_k = k - (k >= bwt->primary);
+	_l = l - (l >= bwt->primary);
+	if (_l>>OCC_INTV_SHIFT != _k>>OCC_INTV_SHIFT || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
+		bwt_occ4(bwt, k, cntk);
+		bwt_occ4(bwt, l, cntl);
+	} else {
+		bwtint_t x, y;
+		uint32_t *p, tmp, *endk, *endl;
+		k -= (k >= bwt->primary); // because $ is not in bwt
+		l -= (l >= bwt->primary);
+		p = bwt_occ_intv(bwt, k);
+		memcpy(cntk, p, 4 * sizeof(bwtint_t));
+		p += sizeof(bwtint_t); // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
+		// prepare cntk[]
+		endk = p + ((k>>4) - ((k&~OCC_INTV_MASK)>>4));
+		endl = p + ((l>>4) - ((l&~OCC_INTV_MASK)>>4));
+		for (x = 0; p < endk; ++p) x += __occ_aux4(bwt, *p);
+		y = x;
+		tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
+		x += __occ_aux4(bwt, tmp) - (~k&15);
+		// calculate cntl[] and finalize cntk[]
+		for (; p < endl; ++p) y += __occ_aux4(bwt, *p);
+		tmp = *p & ~((1U<<((~l&15)<<1)) - 1);
+		y += __occ_aux4(bwt, tmp) - (~l&15);
+		memcpy(cntl, cntk, 4 * sizeof(bwtint_t));
+		cntk[0] += x&0xff; cntk[1] += x>>8&0xff; cntk[2] += x>>16&0xff; cntk[3] += x>>24;
+		cntl[0] += y&0xff; cntl[1] += y>>8&0xff; cntl[2] += y>>16&0xff; cntl[3] += y>>24;
+	}
+}
+
+int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end)
+{
+	bwtint_t k, l, ok, ol;
+	int i;
+	k = 0; l = bwt->seq_len;
+	for (i = len - 1; i >= 0; --i) {
+		ubyte_t c = str[i];
+		if (c > 3) return 0; // no match
+		bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
+		k = bwt->L2[c] + ok + 1;
+		l = bwt->L2[c] + ol;
+		if (k > l) break; // no match
+	}
+	if (k > l) return 0; // no match
+	if (sa_begin) *sa_begin = k;
+	if (sa_end)   *sa_end = l;
+	return l - k + 1;
+}
+
+int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0)
+{
+	int i;
+	bwtint_t k, l, ok, ol;
+	k = *k0; l = *l0;
+	for (i = len - 1; i >= 0; --i) {
+		ubyte_t c = str[i];
+		if (c > 3) return 0; // there is an N here. no match
+		bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
+		k = bwt->L2[c] + ok + 1;
+		l = bwt->L2[c] + ol;
+		if (k > l) return 0; // no match
+	}
+	*k0 = k; *l0 = l;
+	return l - k + 1;
+}
+
+/*********************
+ * Bidirectional BWT *
+ *********************/
+
+void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back)
+{
+	bwtint_t tk[4], tl[4];
+	int i;
+	bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
+	for (i = 0; i != 4; ++i) {
+		ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i];
+		ok[i].x[2] = tl[i] - tk[i];
+	}
+	ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
+	ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
+	ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
+	ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
+}
+
+static void bwt_reverse_intvs(bwtintv_v *p)
+{
+	if (p->n > 1) {
+		int j;
+		for (j = 0; j < p->n>>1; ++j) {
+			bwtintv_t tmp = p->a[p->n - 1 - j];
+			p->a[p->n - 1 - j] = p->a[j];
+			p->a[j] = tmp;
+		}
+	}
+}
+// NOTE: $max_intv is not currently used in BWA-MEM
+// 找smem（seed）
+int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, uint64_t max_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2])
+{
+	int i, j, c, ret;
+	bwtintv_t ik, ok[4];
+	bwtintv_v a[2], *prev, *curr, *swap;
+
+	mem->n = 0;
+	if (q[x] > 3) return x + 1;
+	if (min_intv < 1) min_intv = 1; // the interval size should be at least 1
+	kv_init(a[0]); kv_init(a[1]);
+	prev = tmpvec && tmpvec[0]? tmpvec[0] : &a[0]; // use the temporary vector if provided
+	curr = tmpvec && tmpvec[1]? tmpvec[1] : &a[1];
+	bwt_set_intv(bwt, q[x], ik); // the initial interval of a single base
+	ik.info = x + 1;
+
+	for (i = x + 1, curr->n = 0; i < len; ++i) { // forward search
+		if (ik.x[2] < max_intv) { // an interval small enough
+			kv_push(bwtintv_t, *curr, ik);
+			break;
+		} else if (q[i] < 4) { // an A/C/G/T base
+			c = 3 - q[i]; // complement of q[i]
+			bwt_extend(bwt, &ik, ok, 0);
+			if (ok[c].x[2] != ik.x[2]) { // change of the interval size
+				kv_push(bwtintv_t, *curr, ik);
+				if (ok[c].x[2] < min_intv) break; // the interval size is too small to be extended further
+			}
+			ik = ok[c]; ik.info = i + 1;
+		} else { // an ambiguous base
+			kv_push(bwtintv_t, *curr, ik);
+			break; // always terminate extension at an ambiguous base; in this case, i<len always stands
+		}
+	}
+	if (i == len) kv_push(bwtintv_t, *curr, ik); // push the last interval if we reach the end
+	bwt_reverse_intvs(curr); // s.t. smaller intervals (i.e. longer matches) visited first
+	ret = curr->a[0].info; // this will be the returned value
+	swap = curr; curr = prev; prev = swap;
+
+	for (i = x - 1; i >= -1; --i) { // backward search for MEMs
+		c = i < 0? -1 : q[i] < 4? q[i] : -1; // c==-1 if i<0 or q[i] is an ambiguous base
+		for (j = 0, curr->n = 0; j < prev->n; ++j) {
+			bwtintv_t *p = &prev->a[j];
+			if (c >= 0 && ik.x[2] >= max_intv) bwt_extend(bwt, p, ok, 1);
+			if (c < 0 || ik.x[2] < max_intv || ok[c].x[2] < min_intv) { // keep the hit if reaching the beginning or an ambiguous base or the intv is small enough
+				if (curr->n == 0) { // test curr->n>0 to make sure there are no longer matches
+					if (mem->n == 0 || i + 1 < mem->a[mem->n-1].info>>32) { // skip contained matches
+						ik = *p; ik.info |= (uint64_t)(i + 1)<<32;
+						kv_push(bwtintv_t, *mem, ik);
+					}
+				} // otherwise the match is contained in another longer match
+			} else if (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2]) {
+				ok[c].info = p->info;
+				kv_push(bwtintv_t, *curr, ok[c]);
+			}
+		}
+		if (curr->n == 0) break;
+		swap = curr; curr = prev; prev = swap;
+	}
+	bwt_reverse_intvs(mem); // s.t. sorted by the start coordinate
+
+	if (tmpvec == 0 || tmpvec[0] == 0) free(a[0].a);
+	if (tmpvec == 0 || tmpvec[1] == 0) free(a[1].a);
+	return ret;
+}
+
+int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2])
+{
+	return bwt_smem1a(bwt, len, q, x, min_intv, 0, mem, tmpvec);
+}
+
+int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem)
+{
+	int i, c;
+	bwtintv_t ik, ok[4];
+
+	memset(mem, 0, sizeof(bwtintv_t));
+	if (q[x] > 3) return x + 1;
+	bwt_set_intv(bwt, q[x], ik); // the initial interval of a single base
+	for (i = x + 1; i < len; ++i) { // forward search
+		if (q[i] < 4) { // an A/C/G/T base
+			c = 3 - q[i]; // complement of q[i]
+			bwt_extend(bwt, &ik, ok, 0);
+			if (ok[c].x[2] < max_intv && i - x >= min_len) {
+				*mem = ok[c];
+				mem->info = (uint64_t)x<<32 | (i + 1);
+				return i + 1;
+			}
+			ik = ok[c];
+		} else return i + 1;
+	}
+	return len;
+}
+
+/*************************
+ * Read/write BWT and SA *
+ *************************/
+
+void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
+{
+	FILE *fp;
+	fp = xopen(fn, "wb");
+	err_fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	err_fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
+	err_fflush(fp);
+	err_fclose(fp);
+}
+
+void bwt_dump_sa(const char *fn, const bwt_t *bwt)
+{
+	FILE *fp;
+	fp = xopen(fn, "wb");
+	err_fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	err_fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	err_fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
+	err_fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
+	err_fflush(fp);
+	err_fclose(fp);
+}
+
+static bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
+{ // Mac/Darwin has a bug when reading data longer than 2GB. This function fixes this issue by reading data in small chunks
+	const int bufsize = 0x1000000; // 16M block
+	bwtint_t offset = 0;
+	while (size) {
+		int x = bufsize < size? bufsize : size;
+		if ((x = err_fread_noeof(a + offset, 1, x, fp)) == 0) break;
+		size -= x; offset += x;
+	}
+	return offset;
+}
+
+void bwt_restore_sa(const char *fn, bwt_t *bwt)
+{
+	char skipped[256];
+	FILE *fp;
+	bwtint_t primary;
+
+	fp = xopen(fn, "rb");
+	err_fread_noeof(&primary, sizeof(bwtint_t), 1, fp);
+	xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
+	err_fread_noeof(skipped, sizeof(bwtint_t), 4, fp); // skip
+	err_fread_noeof(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(&primary, sizeof(bwtint_t), 1, fp);
+	xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
+
+	bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
+	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
+	bwt->sa[0] = -1;
+
+	fread_fix(fp, sizeof(bwtint_t) * (bwt->n_sa - 1), bwt->sa + 1);
+	err_fclose(fp);
+}
+
+bwt_t *bwt_restore_bwt(const char *fn)
+{
+	bwt_t *bwt;
+	FILE *fp;
+
+	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
+	fp = xopen(fn, "rb");
+	err_fseek(fp, 0, SEEK_END);
+	bwt->bwt_size = (err_ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
+	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
+	err_fseek(fp, 0, SEEK_SET);
+	err_fread_noeof(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	err_fread_noeof(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	fread_fix(fp, bwt->bwt_size<<2, bwt->bwt);
+	bwt->seq_len = bwt->L2[4];
+	err_fclose(fp);
+	bwt_gen_cnt_table(bwt);
+
+	return bwt;
+}
+
+void bwt_destroy(bwt_t *bwt)
+{
+	if (bwt == 0) return;
+	free(bwt->sa); free(bwt->bwt);
+	free(bwt);
+}

bwt.h

@@ -0,0 +1,132 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <hli@jimmy.harvard.edu> */
+
+#ifndef BWA_BWT_H
+#define BWA_BWT_H
+
+#include <stdint.h>
+#include <stddef.h>
+
+// requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line because some part of the code assume OCC_INTERVAL=0x80
+#define OCC_INTV_SHIFT 7
+#define OCC_INTERVAL   (1LL<<OCC_INTV_SHIFT)
+#define OCC_INTV_MASK  (OCC_INTERVAL - 1)
+
+#ifndef BWA_UBYTE
+#define BWA_UBYTE
+typedef unsigned char ubyte_t;
+#endif
+
+typedef uint64_t bwtint_t;
+
+typedef struct {
+	bwtint_t primary; // S^{-1}(0), or the primary index of BWT
+	bwtint_t L2[5]; // C(), cumulative count
+	bwtint_t seq_len; // sequence length
+	bwtint_t bwt_size; // size of bwt, about seq_len/4
+	uint32_t *bwt; // BWT
+	// occurance array, separated to two parts
+	uint32_t cnt_table[256];
+	// suffix array
+	int sa_intv;
+	bwtint_t n_sa;
+	bwtint_t *sa;
+} bwt_t;
+
+typedef struct {
+	bwtint_t x[3], info;
+} bwtintv_t;
+
+typedef struct { size_t n, m; bwtintv_t *a; } bwtintv_v;
+
+/* For general OCC_INTERVAL, the following is correct:
+#define bwt_bwt(b, k) ((b)->bwt[(k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4) + sizeof(bwtint_t)/4*4 + (k)%OCC_INTERVAL/16])
+#define bwt_occ_intv(b, k) ((b)->bwt + (k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4)
+*/
+
+// The following two lines are ONLY correct when OCC_INTERVAL==0x80
+#define bwt_bwt(b, k) ((b)->bwt[((k)>>7<<4) + sizeof(bwtint_t) + (((k)&0x7f)>>4)])
+#define bwt_occ_intv(b, k) ((b)->bwt + ((k)>>7<<4))
+
+/* retrieve a character from the $-removed BWT string. Note that
+ * bwt_t::bwt is not exactly the BWT string and therefore this macro is
+ * called bwt_B0 instead of bwt_B */
+#define bwt_B0(b, k) (bwt_bwt(b, k)>>((~(k)&0xf)<<1)&3)
+
+#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]-(bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3-(c)]+1, (ik).info = 0)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void bwt_dump_bwt(const char *fn, const bwt_t *bwt);
+	void bwt_dump_sa(const char *fn, const bwt_t *bwt);
+
+	bwt_t *bwt_restore_bwt(const char *fn);
+	void bwt_restore_sa(const char *fn, bwt_t *bwt);
+
+	void bwt_destroy(bwt_t *bwt);
+
+	void bwt_bwtgen(const char *fn_pac, const char *fn_bwt); // from BWT-SW
+	void bwt_bwtgen2(const char *fn_pac, const char *fn_bwt, int block_size); // from BWT-SW
+	void bwt_cal_sa(bwt_t *bwt, int intv);
+
+	void bwt_bwtupdate_core(bwt_t *bwt);
+
+	bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
+	void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
+	bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k);
+
+	// more efficient version of bwt_occ/bwt_occ4 for retrieving two close Occ values
+	void bwt_gen_cnt_table(bwt_t *bwt);
+	void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
+	void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
+
+	int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
+	int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);
+
+	/**
+	 * Extend bi-SA-interval _ik_
+	 */
+	void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back);
+
+	/**
+	 * Given a query _q_, collect potential SMEMs covering position _x_ and store them in _mem_.
+	 * Return the end of the longest exact match starting from _x_.
+	 */
+	int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
+	int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, uint64_t max_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
+
+	int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwt_lite.c

@@ -0,0 +1,98 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include "bwt_lite.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+int is_sa(const uint8_t *T, int *SA, int n);
+int is_bwt(uint8_t *T, int n);
+
+bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
+{
+	bwtl_t *b;
+	int i;
+	b = (bwtl_t*)calloc(1, sizeof(bwtl_t));
+	b->seq_len = len;
+
+	{ // calculate b->bwt
+		uint8_t *s;
+		b->sa = (uint32_t*)calloc(len + 1, 4);
+		is_sa(seq, (int*)b->sa, len);
+		s = (uint8_t*)calloc(len + 1, 1);
+		for (i = 0; i <= len; ++i) {
+			if (b->sa[i] == 0) b->primary = i;
+			else s[i] = seq[b->sa[i] - 1];
+		}
+		for (i = b->primary; i < len; ++i) s[i] = s[i + 1];
+		b->bwt_size = (len + 15) / 16;
+		b->bwt = (uint32_t*)calloc(b->bwt_size, 4);
+		for (i = 0; i < len; ++i)
+			b->bwt[i>>4] |= s[i] << ((15 - (i&15)) << 1);
+		free(s);
+	}
+	{ // calculate b->occ
+		uint32_t c[4];
+		b->n_occ = (len + 15) / 16 * 4;
+		b->occ = (uint32_t*)calloc(b->n_occ, 4);
+		memset(c, 0, 16);
+		for (i = 0; i < len; ++i) {
+			if (i % 16 == 0)
+				memcpy(b->occ + (i/16) * 4, c, 16);
+			++c[bwtl_B0(b, i)];
+		}
+		memcpy(b->L2+1, c, 16);
+		for (i = 2; i < 5; ++i) b->L2[i] += b->L2[i-1];
+	}
+	{ // generate cnt_table
+		for (i = 0; i != 256; ++i) {
+			uint32_t j, x = 0;
+			for (j = 0; j != 4; ++j)
+				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
+			b->cnt_table[i] = x;
+		}
+	}
+	return b;
+}
+uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
+{
+	uint32_t n, b;
+	if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
+	if (k == (uint32_t)(-1)) return 0;
+	if (k >= bwt->primary) --k; // because $ is not in bwt
+	n = bwt->occ[k/16<<2|c];
+	b = bwt->bwt[k/16] & ~((1U<<((15-(k&15))<<1)) - 1);
+	n += (bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
+		  + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]) >> (c<<3) & 0xff;
+	if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
+	return n;
+}
+void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
+{
+	uint32_t x, b;
+	if (k == (uint32_t)(-1)) {
+		memset(cnt, 0, 16);
+		return;
+	}
+	if (k >= bwt->primary) --k; // because $ is not in bwt
+	memcpy(cnt, bwt->occ + (k>>4<<2), 16);
+	b = bwt->bwt[k>>4] & ~((1U<<((~k&15)<<1)) - 1);
+	x = bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
+		+ bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24];
+	x -= 15 - (k&15);
+	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
+}
+void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
+{
+	bwtl_occ4(bwt, k, cntk);
+	bwtl_occ4(bwt, l, cntl);
+}
+void bwtl_destroy(bwtl_t *bwt)
+{
+	if (bwt) {
+		free(bwt->occ); free(bwt->bwt); free(bwt->sa);
+		free(bwt);
+	}
+}

bwt_lite.h

@@ -0,0 +1,29 @@
+#ifndef BWT_LITE_H_
+#define BWT_LITE_H_
+
+#include <stdint.h>
+
+typedef struct {
+	uint32_t seq_len, bwt_size, n_occ;
+	uint32_t primary;
+	uint32_t *bwt, *occ, *sa, L2[5];
+	uint32_t cnt_table[256];
+} bwtl_t;
+
+#define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
+	uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
+	void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
+	void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
+	void bwtl_destroy(bwtl_t *bwt);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwtaln.c

@@ -0,0 +1,321 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include <stdint.h>
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+#include "bwtaln.h"
+#include "bwtgap.h"
+#include "utils.h"
+#include "bwa.h"
+
+#ifdef HAVE_PTHREAD
+#include <pthread.h>
+#endif
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+gap_opt_t *gap_init_opt()
+{
+	gap_opt_t *o;
+	o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
+	/* IMPORTANT: s_mm*10 should be about the average base error
+	   rate. Voilating this requirement will break pairing! */
+	o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
+	o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
+	o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
+	o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
+	o->seed_len = 32; o->max_seed_diff = 2;
+	o->fnr = 0.04;
+	o->n_threads = 1;
+	o->max_top2 = 30;
+	o->trim_qual = 0;
+	return o;
+}
+
+int bwa_cal_maxdiff(int l, double err, double thres)
+{
+	double elambda = exp(-l * err);
+	double sum, y = 1.0;
+	int k, x = 1;
+	for (k = 1, sum = elambda; k < 1000; ++k) {
+		y *= l * err;
+		x *= k;
+		sum += elambda * y / x;
+		if (1.0 - sum < thres) return k;
+	}
+	return 2;
+}
+
+// width must be filled as zero
+int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width)
+{
+	bwtint_t k, l, ok, ol;
+	int i, bid;
+	bid = 0;
+	k = 0; l = bwt->seq_len;
+	for (i = 0; i < len; ++i) {
+		ubyte_t c = str[i];
+		if (c < 4) {
+			bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
+			k = bwt->L2[c] + ok + 1;
+			l = bwt->L2[c] + ol;
+		}
+		if (k > l || c > 3) { // then restart
+			k = 0;
+			l = bwt->seq_len;
+			++bid;
+		}
+		width[i].w = l - k + 1;
+		width[i].bid = bid;
+	}
+	width[len].w = 0;
+	width[len].bid = ++bid;
+	return bid;
+}
+
+void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
+{
+	int i, j, max_l = 0, max_len;
+	gap_stack_t *stack;
+	bwt_width_t *w, *seed_w;
+	gap_opt_t local_opt = *opt;
+
+	// initiate priority stack
+	for (i = max_len = 0; i != n_seqs; ++i)
+		if (seqs[i].len > max_len) max_len = seqs[i].len;
+	if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
+	if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
+	stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
+
+	seed_w = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
+	w = 0;
+	for (i = 0; i != n_seqs; ++i) {
+		bwa_seq_t *p = seqs + i;
+#ifdef HAVE_PTHREAD
+		if (i % opt->n_threads != tid) continue;
+#endif
+		p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
+		if (max_l < p->len) {
+			max_l = p->len;
+			w = (bwt_width_t*)realloc(w, (max_l + 1) * sizeof(bwt_width_t));
+			memset(w, 0, (max_l + 1) * sizeof(bwt_width_t));
+		}
+		bwt_cal_width(bwt, p->len, p->seq, w);
+		if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
+		local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
+		if (p->len > opt->seed_len)
+			bwt_cal_width(bwt, opt->seed_len, p->seq + (p->len - opt->seed_len), seed_w);
+		// core function
+		for (j = 0; j < p->len; ++j) // we need to complement
+			p->seq[j] = p->seq[j] > 3? 4 : 3 - p->seq[j];
+		p->aln = bwt_match_gap(bwt, p->len, p->seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
+		//fprintf(stderr, "mm=%lld,ins=%lld,del=%lld,gapo=%lld\n", p->aln->n_mm, p->aln->n_ins, p->aln->n_del, p->aln->n_gapo);
+		// clean up the unused data in the record
+		free(p->name); free(p->seq); free(p->rseq); free(p->qual);
+		p->name = 0; p->seq = p->rseq = p->qual = 0;
+	}
+	free(seed_w); free(w);
+	gap_destroy_stack(stack);
+}
+
+#ifdef HAVE_PTHREAD
+typedef struct {
+	int tid;
+	bwt_t *bwt;
+	int n_seqs;
+	bwa_seq_t *seqs;
+	const gap_opt_t *opt;
+} thread_aux_t;
+
+static void *worker(void *data)
+{
+	thread_aux_t *d = (thread_aux_t*)data;
+	bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
+	return 0;
+}
+#endif
+
+bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
+{
+	bwa_seqio_t *ks;
+	if (mode & BWA_MODE_BAM) { // open BAM
+		int which = 0;
+		if (mode & BWA_MODE_BAM_SE) which |= 4;
+		if (mode & BWA_MODE_BAM_READ1) which |= 1;
+		if (mode & BWA_MODE_BAM_READ2) which |= 2;
+		if (which == 0) which = 7; // then read all reads
+		ks = bwa_bam_open(fn_fa, which);
+	} else ks = bwa_seq_open(fn_fa);
+	return ks;
+}
+
+void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
+{
+	int i, n_seqs;
+	long long tot_seqs = 0;
+	bwa_seq_t *seqs;
+	bwa_seqio_t *ks;
+	clock_t t;
+	bwt_t *bwt;
+
+	// initialization
+	ks = bwa_open_reads(opt->mode, fn_fa);
+
+	{ // load BWT
+		char *str = (char*)calloc(strlen(prefix) + 10, 1);
+		strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
+		free(str);
+	}
+
+	// core loop
+	err_fwrite(SAI_MAGIC, 1, 4, stdout);
+	err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
+	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
+		tot_seqs += n_seqs;
+		t = clock();
+
+		fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");
+
+#ifdef HAVE_PTHREAD
+		if (opt->n_threads <= 1) { // no multi-threading at all
+			bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
+		} else {
+			pthread_t *tid;
+			pthread_attr_t attr;
+			thread_aux_t *data;
+			int j;
+			pthread_attr_init(&attr);
+			pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+			data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
+			tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
+			for (j = 0; j < opt->n_threads; ++j) {
+				data[j].tid = j; data[j].bwt = bwt;
+				data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
+				pthread_create(&tid[j], &attr, worker, data + j);
+			}
+			for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
+			free(data); free(tid);
+		}
+#else
+		bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
+#endif
+
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+
+		t = clock();
+		fprintf(stderr, "[bwa_aln_core] write to the disk... ");
+		for (i = 0; i < n_seqs; ++i) {
+			bwa_seq_t *p = seqs + i;
+			err_fwrite(&p->n_aln, 4, 1, stdout);
+			if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
+		}
+		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+
+		bwa_free_read_seq(n_seqs, seqs);
+		fprintf(stderr, "[bwa_aln_core] %lld sequences have been processed.\n", tot_seqs);
+	}
+
+	// destroy
+	bwt_destroy(bwt);
+	bwa_seq_close(ks);
+}
+
+int bwa_aln(int argc, char *argv[])
+{
+	int c, opte = -1;
+	gap_opt_t *opt;
+	char *prefix;
+
+	opt = gap_init_opt();
+	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:LR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
+		switch (c) {
+		case 'n':
+			if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
+			else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
+			break;
+		case 'o': opt->max_gapo = atoi(optarg); break;
+		case 'e': opte = atoi(optarg); break;
+		case 'M': opt->s_mm = atoi(optarg); break;
+		case 'O': opt->s_gapo = atoi(optarg); break;
+		case 'E': opt->s_gape = atoi(optarg); break;
+		case 'd': opt->max_del_occ = atoi(optarg); break;
+		case 'i': opt->indel_end_skip = atoi(optarg); break;
+		case 'l': opt->seed_len = atoi(optarg); break;
+		case 'k': opt->max_seed_diff = atoi(optarg); break;
+		case 'm': opt->max_entries = atoi(optarg); break;
+		case 't': opt->n_threads = atoi(optarg); break;
+		case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
+		case 'R': opt->max_top2 = atoi(optarg); break;
+		case 'q': opt->trim_qual = atoi(optarg); break;
+		case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
+		case 'f': xreopen(optarg, "wb", stdout); break;
+		case 'b': opt->mode |= BWA_MODE_BAM; break;
+		case '0': opt->mode |= BWA_MODE_BAM_SE; break;
+		case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
+		case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
+		case 'I': opt->mode |= BWA_MODE_IL13; break;
+		case 'Y': opt->mode |= BWA_MODE_CFY; break;
+		case 'B': opt->mode |= atoi(optarg) << 24; break;
+		default: return 1;
+		}
+	}
+	if (opte > 0) {
+		opt->max_gape = opte;
+		opt->mode &= ~BWA_MODE_GAPE;
+	}
+
+	if (optind + 2 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa aln [options] <prefix> <in.fq>\n\n");
+		fprintf(stderr, "Options: -n NUM    max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
+				BWA_AVG_ERR, opt->fnr);
+		fprintf(stderr, "         -o INT    maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
+		fprintf(stderr, "         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
+		fprintf(stderr, "         -i INT    do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
+		fprintf(stderr, "         -d INT    maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
+		fprintf(stderr, "         -l INT    seed length [%d]\n", opt->seed_len);
+		fprintf(stderr, "         -k INT    maximum differences in the seed [%d]\n", opt->max_seed_diff);
+		fprintf(stderr, "         -m INT    maximum entries in the queue [%d]\n", opt->max_entries);
+		fprintf(stderr, "         -t INT    number of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "         -M INT    mismatch penalty [%d]\n", opt->s_mm);
+		fprintf(stderr, "         -O INT    gap open penalty [%d]\n", opt->s_gapo);
+		fprintf(stderr, "         -E INT    gap extension penalty [%d]\n", opt->s_gape);
+		fprintf(stderr, "         -R INT    stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
+		fprintf(stderr, "         -q INT    quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
+        fprintf(stderr, "         -f FILE   file to write output to instead of stdout\n");
+		fprintf(stderr, "         -B INT    length of barcode\n");
+		fprintf(stderr, "         -L        log-scaled gap penalty for long deletions\n");
+		fprintf(stderr, "         -N        non-iterative mode: search for all n-difference hits (slooow)\n");
+		fprintf(stderr, "         -I        the input is in the Illumina 1.3+ FASTQ-like format\n");
+		fprintf(stderr, "         -b        the input read file is in the BAM format\n");
+		fprintf(stderr, "         -0        use single-end reads only (effective with -b)\n");
+		fprintf(stderr, "         -1        use the 1st read in a pair (effective with -b)\n");
+		fprintf(stderr, "         -2        use the 2nd read in a pair (effective with -b)\n");
+		fprintf(stderr, "         -Y        filter Casava-filtered sequences\n");
+		fprintf(stderr, "\n");
+		return 1;
+	}
+	if (opt->fnr > 0.0) {
+		int i, k;
+		for (i = 17, k = 0; i <= 250; ++i) {
+			int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
+			if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
+			k = l;
+		}
+	}
+	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
+		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
+		free(opt);
+		return 1;
+	}
+	bwa_aln_core(prefix, argv[optind+1], opt);
+	free(opt); free(prefix);
+	return 0;
+}

bwtaln.h

@@ -0,0 +1,153 @@
+#ifndef BWTALN_H
+#define BWTALN_H
+
+#include <stdint.h>
+#include "bwt.h"
+
+#define BWA_TYPE_NO_MATCH 0
+#define BWA_TYPE_UNIQUE 1
+#define BWA_TYPE_REPEAT 2
+#define BWA_TYPE_MATESW 3
+
+#define SAM_FPD   1 // paired
+#define SAM_FPP   2 // properly paired
+#define SAM_FSU   4 // self-unmapped
+#define SAM_FMU   8 // mate-unmapped
+#define SAM_FSR  16 // self on the reverse strand
+#define SAM_FMR  32 // mate on the reverse strand
+#define SAM_FR1  64 // this is read one
+#define SAM_FR2 128 // this is read two
+#define SAM_FSC 256 // secondary alignment
+
+#define BWA_AVG_ERR 0.02
+#define BWA_MIN_RDLEN 35 // for read trimming
+
+#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
+
+#ifndef bns_pac
+#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
+#endif
+
+#define FROM_M 0
+#define FROM_I 1
+#define FROM_D 2
+#define FROM_S 3
+
+#define SAI_MAGIC "SAI\1"
+
+typedef struct {
+	bwtint_t w;
+	int bid;
+} bwt_width_t;
+
+typedef struct {
+	uint64_t n_mm:8, n_gapo:8, n_gape:8, score:20, n_ins:10, n_del:10;
+	bwtint_t k, l;
+} bwt_aln1_t;
+
+typedef uint16_t bwa_cigar_t;
+/* rgoya: If changing order of bytes, beware of operations like:
+ *     s->cigar[0] += s->full_len - s->len;
+ */
+#define CIGAR_OP_SHIFT 14
+#define CIGAR_LN_MASK 0x3fff
+
+#define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
+#define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
+#define __cigar_create(__op, __len) ((__op)<<CIGAR_OP_SHIFT | (__len))
+
+typedef struct {
+	uint32_t n_cigar:15, gap:8, mm:8, strand:1;
+	int ref_shift;
+	bwtint_t pos;
+	bwa_cigar_t *cigar;
+} bwt_multi1_t;
+
+typedef struct {
+	char *name;
+	ubyte_t *seq, *rseq, *qual;
+	uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
+	uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;
+	int score;
+	int clip_len;
+	// alignments in SA coordinates
+	int n_aln;
+	bwt_aln1_t *aln;
+	// multiple hits
+	int n_multi;
+	bwt_multi1_t *multi;
+	// alignment information
+	bwtint_t sa, pos;
+	uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
+	int ref_shift;
+	int n_cigar;
+	bwa_cigar_t *cigar;
+	// for multi-threading only
+	int tid;
+	// barcode
+	char bc[BWA_MAX_BCLEN+1]; // null terminated; up to BWA_MAX_BCLEN bases
+	// NM and MD tags
+	uint32_t full_len:20, nm:12;
+	char *md;
+} bwa_seq_t;
+
+#define BWA_MODE_GAPE       0x01
+#define BWA_MODE_COMPREAD   0x02
+#define BWA_MODE_LOGGAP     0x04
+#define BWA_MODE_CFY        0x08
+#define BWA_MODE_NONSTOP    0x10
+#define BWA_MODE_BAM        0x20
+#define BWA_MODE_BAM_SE     0x40
+#define BWA_MODE_BAM_READ1  0x80
+#define BWA_MODE_BAM_READ2  0x100
+#define BWA_MODE_IL13       0x200
+
+typedef struct {
+	int s_mm, s_gapo, s_gape;
+	int mode; // bit 24-31 are the barcode length
+	int indel_end_skip, max_del_occ, max_entries;
+	float fnr;
+	int max_diff, max_gapo, max_gape;
+	int max_seed_diff, seed_len;
+	int n_threads;
+	int max_top2;
+	int trim_qual;
+} gap_opt_t;
+
+#define BWA_PET_STD   1
+
+typedef struct {
+	int max_isize, force_isize;
+	int max_occ;
+	int n_multi, N_multi;
+	int type, is_sw, is_preload;
+	double ap_prior;
+} pe_opt_t;
+
+struct __bwa_seqio_t;
+typedef struct __bwa_seqio_t bwa_seqio_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	gap_opt_t *gap_init_opt();
+	void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);
+
+	bwa_seqio_t *bwa_seq_open(const char *fn);
+	bwa_seqio_t *bwa_bam_open(const char *fn, int which);
+	void bwa_seq_close(bwa_seqio_t *bs);
+	void seq_reverse(int len, ubyte_t *seq, int is_comp);
+	bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
+	void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
+
+	int bwa_cal_maxdiff(int l, double err, double thres);
+	void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);
+
+	void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwtgap.c

@@ -0,0 +1,264 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "bwtgap.h"
+#include "bwtaln.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define STATE_M 0
+#define STATE_I 1
+#define STATE_D 2
+
+#define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)
+
+gap_stack_t *gap_init_stack2(int max_score)
+{
+	gap_stack_t *stack;
+	stack = (gap_stack_t*)calloc(1, sizeof(gap_stack_t));
+	stack->n_stacks = max_score;
+	stack->stacks = (gap_stack1_t*)calloc(stack->n_stacks, sizeof(gap_stack1_t));
+	return stack;
+}
+
+gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
+{
+	return gap_init_stack2(aln_score(max_mm+1, max_gapo+1, max_gape+1, opt));
+}
+
+void gap_destroy_stack(gap_stack_t *stack)
+{
+	int i;
+	for (i = 0; i != stack->n_stacks; ++i) free(stack->stacks[i].stack);
+	free(stack->stacks);
+	free(stack);
+}
+
+static void gap_reset_stack(gap_stack_t *stack)
+{
+	int i;
+	for (i = 0; i != stack->n_stacks; ++i)
+		stack->stacks[i].n_entries = 0;
+	stack->best = stack->n_stacks;
+	stack->n_entries = 0;
+}
+
+static inline void gap_push(gap_stack_t *stack, int i, bwtint_t k, bwtint_t l, int n_mm, int n_gapo, int n_gape, int n_ins, int n_del,
+							int state, int is_diff, const gap_opt_t *opt)
+{
+	int score;
+	gap_entry_t *p;
+	gap_stack1_t *q;
+	score = aln_score(n_mm, n_gapo, n_gape, opt);
+	q = stack->stacks + score;
+	if (q->n_entries == q->m_entries) {
+		q->m_entries = q->m_entries? q->m_entries<<1 : 4;
+		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
+	}
+	p = q->stack + q->n_entries;
+	p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l;
+	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape;
+	p->n_ins = n_ins; p->n_del = n_del;
+	p->state = state; 
+	p->last_diff_pos = is_diff? i : 0;
+	++(q->n_entries);
+	++(stack->n_entries);
+	if (stack->best > score) stack->best = score;
+}
+
+static inline void gap_pop(gap_stack_t *stack, gap_entry_t *e)
+{
+	gap_stack1_t *q;
+	q = stack->stacks + stack->best;
+	*e = q->stack[q->n_entries - 1];
+	--(q->n_entries);
+	--(stack->n_entries);
+	if (q->n_entries == 0 && stack->n_entries) { // reset best
+		int i;
+		for (i = stack->best + 1; i < stack->n_stacks; ++i)
+			if (stack->stacks[i].n_entries != 0) break;
+		stack->best = i;
+	} else if (stack->n_entries == 0) stack->best = stack->n_stacks;
+}
+
+static inline void gap_shadow(int x, int len, bwtint_t max, int last_diff_pos, bwt_width_t *w)
+{
+	int i, j;
+	for (i = j = 0; i < last_diff_pos; ++i) {
+		if (w[i].w > x) w[i].w -= x;
+		else if (w[i].w == x) {
+			w[i].bid = 1;
+			w[i].w = max - (++j);
+		} // else should not happen
+	}
+}
+
+static inline int int_log2(uint32_t v)
+{
+	int c = 0;
+	if (v & 0xffff0000u) { v >>= 16; c |= 16; }
+	if (v & 0xff00) { v >>= 8; c |= 8; }
+	if (v & 0xf0) { v >>= 4; c |= 4; }
+	if (v & 0xc) { v >>= 2; c |= 2; }
+	if (v & 0x2) c |= 1;
+	return c;
+}
+
+bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *width,
+						  bwt_width_t *seed_width, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack)
+{ // $seq is the reverse complement of the input read
+	int best_score = aln_score(opt->max_diff+1, opt->max_gapo+1, opt->max_gape+1, opt);
+	int best_diff = opt->max_diff + 1, max_diff = opt->max_diff;
+	int best_cnt = 0;
+	int max_entries = 0, j, _j, n_aln, m_aln;
+	bwt_aln1_t *aln;
+
+	m_aln = 4; n_aln = 0;
+	aln = (bwt_aln1_t*)calloc(m_aln, sizeof(bwt_aln1_t));
+
+	// check whether there are too many N
+	for (j = _j = 0; j < len; ++j)
+		if (seq[j] > 3) ++_j;
+	if (_j > max_diff) {
+		*_n_aln = n_aln;
+		return aln;
+	}
+
+	//for (j = 0; j != len; ++j) printf("#0 %d: [%d,%u]\t[%d,%u]\n", j, w[0][j].bid, w[0][j].w, w[1][j].bid, w[1][j].w);
+	gap_reset_stack(stack); // reset stack
+	gap_push(stack, len, 0, bwt->seq_len, 0, 0, 0, 0, 0, 0, 0, opt);
+
+	while (stack->n_entries) {
+		gap_entry_t e;
+		int i, m, m_seed = 0, hit_found, allow_diff, allow_M, tmp;
+		bwtint_t k, l, cnt_k[4], cnt_l[4], occ;
+
+		if (max_entries < stack->n_entries) max_entries = stack->n_entries;
+		if (stack->n_entries > opt->max_entries) break;
+		gap_pop(stack, &e); // get the best entry
+		k = e.k; l = e.l; // SA interval
+		i = e.info&0xffff; // length
+		if (!(opt->mode & BWA_MODE_NONSTOP) && e.info>>21 > best_score + opt->s_mm) break; // no need to proceed
+
+		m = max_diff - (e.n_mm + e.n_gapo);
+		if (opt->mode & BWA_MODE_GAPE) m -= e.n_gape;
+		if (m < 0) continue;
+		if (seed_width) { // apply seeding
+			m_seed = opt->max_seed_diff - (e.n_mm + e.n_gapo);
+			if (opt->mode & BWA_MODE_GAPE) m_seed -= e.n_gape;
+		}
+		//printf("#1\t[%d,%d,%d,%c]\t[%d,%d,%d]\t[%u,%u]\t[%u,%u]\t%d\n", stack->n_entries, a, i, "MID"[e.state], e.n_mm, e.n_gapo, e.n_gape, width[i-1].bid, width[i-1].w, k, l, e.last_diff_pos);
+		if (i > 0 && m < width[i-1].bid) continue;
+
+		// check whether a hit is found
+		hit_found = 0;
+		if (i == 0) hit_found = 1;
+		else if (m == 0 && (e.state == STATE_M || (opt->mode&BWA_MODE_GAPE) || e.n_gape == opt->max_gape)) { // no diff allowed
+			if (bwt_match_exact_alt(bwt, i, seq, &k, &l)) hit_found = 1;
+			else continue; // no hit, skip
+		}
+
+		if (hit_found) { // action for found hits
+			int score = aln_score(e.n_mm, e.n_gapo, e.n_gape, opt);
+			int do_add = 1;
+			//printf("#2 hits found: %d:(%u,%u)\n", e.n_mm+e.n_gapo, k, l);
+			if (n_aln == 0) {
+				best_score = score;
+				best_diff = e.n_mm + e.n_gapo;
+				if (opt->mode & BWA_MODE_GAPE) best_diff += e.n_gape;
+				if (!(opt->mode & BWA_MODE_NONSTOP))
+					max_diff = (best_diff + 1 > opt->max_diff)? opt->max_diff : best_diff + 1; // top2 behaviour
+			}
+			if (score == best_score) best_cnt += l - k + 1;
+			else if (best_cnt > opt->max_top2) break; // top2b behaviour
+			if (e.n_gapo) { // check whether the hit has been found. this may happen when a gap occurs in a tandem repeat
+				for (j = 0; j != n_aln; ++j)
+					if (aln[j].k == k && aln[j].l == l) break;
+				if (j < n_aln) do_add = 0;
+			}
+			if (do_add) { // append
+				bwt_aln1_t *p;
+				gap_shadow(l - k + 1, len, bwt->seq_len, e.last_diff_pos, width);
+				if (n_aln == m_aln) {
+					m_aln <<= 1;
+					aln = (bwt_aln1_t*)realloc(aln, m_aln * sizeof(bwt_aln1_t));
+					memset(aln + m_aln/2, 0, m_aln/2*sizeof(bwt_aln1_t));
+				}
+				p = aln + n_aln;
+				p->n_mm = e.n_mm; p->n_gapo = e.n_gapo; p->n_gape = e.n_gape;
+				p->n_ins = e.n_ins; p->n_del = e.n_del;
+				p->k = k; p->l = l;
+				p->score = score;
+				//fprintf(stderr, "*** n_mm=%d,n_gapo=%d,n_gape=%d,n_ins=%d,n_del=%d\n", e.n_mm, e.n_gapo, e.n_gape, e.n_ins, e.n_del);
+				++n_aln;
+			}
+			continue;
+		}
+
+		--i;
+		bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values
+		occ = l - k + 1;
+		// test whether diff is allowed
+		allow_diff = allow_M = 1;
+		if (i > 0) {
+			int ii = i - (len - opt->seed_len);
+			if (width[i-1].bid > m-1) allow_diff = 0;
+			else if (width[i-1].bid == m-1 && width[i].bid == m-1 && width[i-1].w == width[i].w) allow_M = 0;
+			if (seed_width && ii > 0) {
+				if (seed_width[ii-1].bid > m_seed-1) allow_diff = 0;
+				else if (seed_width[ii-1].bid == m_seed-1 && seed_width[ii].bid == m_seed-1
+						 && seed_width[ii-1].w == seed_width[ii].w) allow_M = 0;
+			}
+		}
+		// indels
+		tmp = (opt->mode & BWA_MODE_LOGGAP)? int_log2(e.n_gape + e.n_gapo)/2+1 : e.n_gapo + e.n_gape;
+		if (allow_diff && i >= opt->indel_end_skip + tmp && len - i >= opt->indel_end_skip + tmp) {
+			if (e.state == STATE_M) { // gap open
+				if (e.n_gapo < opt->max_gapo) { // gap open is allowed
+					// insertion
+					gap_push(stack, i, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, e.n_ins + 1, e.n_del, STATE_I, 1, opt);
+					// deletion
+					for (j = 0; j != 4; ++j) {
+						k = bwt->L2[j] + cnt_k[j] + 1;
+						l = bwt->L2[j] + cnt_l[j];
+						if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, e.n_ins, e.n_del + 1, STATE_D, 1, opt);
+					}
+				}
+			} else if (e.state == STATE_I) { // extention of an insertion
+				if (e.n_gape < opt->max_gape) // gap extention is allowed
+					gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, e.n_ins + 1, e.n_del, STATE_I, 1, opt);
+			} else if (e.state == STATE_D) { // extention of a deletion
+				if (e.n_gape < opt->max_gape) { // gap extention is allowed
+					if (e.n_gape + e.n_gapo < max_diff || occ < opt->max_del_occ) {
+						for (j = 0; j != 4; ++j) {
+							k = bwt->L2[j] + cnt_k[j] + 1;
+							l = bwt->L2[j] + cnt_l[j];
+							if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, e.n_ins, e.n_del + 1, STATE_D, 1, opt);
+						}
+					}
+				}
+			}
+		}
+		// mismatches
+		if (allow_diff && allow_M) { // mismatch is allowed
+			for (j = 1; j <= 4; ++j) {
+				int c = (seq[i] + j) & 3;
+				int is_mm = (j != 4 || seq[i] > 3);
+				k = bwt->L2[c] + cnt_k[c] + 1;
+				l = bwt->L2[c] + cnt_l[c];
+				if (k <= l) gap_push(stack, i, k, l, e.n_mm + is_mm, e.n_gapo, e.n_gape, e.n_ins, e.n_del, STATE_M, is_mm, opt);
+			}
+		} else if (seq[i] < 4) { // try exact match only
+			int c = seq[i] & 3;
+			k = bwt->L2[c] + cnt_k[c] + 1;
+			l = bwt->L2[c] + cnt_l[c];
+			if (k <= l) gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape, e.n_ins, e.n_del, STATE_M, 0, opt);
+		}
+	}
+
+	*_n_aln = n_aln;
+	//fprintf(stderr, "max_entries = %d\n", max_entries);
+	return aln;
+}

bwtgap.h

@@ -0,0 +1,40 @@
+#ifndef BWTGAP_H_
+#define BWTGAP_H_
+
+#include "bwt.h"
+#include "bwtaln.h"
+
+typedef struct { // recursion stack
+	uint32_t info; // score<<21 | i
+	uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
+	uint32_t n_ins:16, n_del:16;
+	int last_diff_pos;
+	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
+} gap_entry_t;
+
+typedef struct {
+	int n_entries, m_entries;
+	gap_entry_t *stack;
+} gap_stack1_t;
+
+typedef struct {
+	int n_stacks, best, n_entries;
+	gap_stack1_t *stacks;
+} gap_stack_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	gap_stack_t *gap_init_stack2(int max_score);
+	gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
+	void gap_destroy_stack(gap_stack_t *stack);
+	bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w,
+							  bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
+	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwtindex.c

@@ -0,0 +1,323 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <time.h>
+#include <zlib.h>
+#include "bntseq.h"
+#include "bwa.h"
+#include "bwt.h"
+#include "utils.h"
+#include "rle.h"
+#include "rope.h"
+
+#ifdef _DIVBWT
+#include "divsufsort.h"
+#endif
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
+int is_bwt(ubyte_t *T, int n);
+
+int64_t bwa_seq_len(const char *fn_pac)
+{
+	FILE *fp;
+	int64_t pac_len;
+	ubyte_t c;
+	fp = xopen(fn_pac, "rb");
+	err_fseek(fp, -1, SEEK_END);
+	pac_len = err_ftell(fp);
+	err_fread_noeof(&c, 1, 1, fp);
+	err_fclose(fp);
+	return (pac_len - 1) * 4 + (int)c;
+}
+
+bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is)
+{
+	bwt_t *bwt;
+	ubyte_t *buf, *buf2;
+	int64_t i, pac_size;
+	FILE *fp;
+
+	// initialization
+	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
+	bwt->seq_len = bwa_seq_len(fn_pac);
+	bwt->bwt_size = (bwt->seq_len + 15) >> 4;
+	fp = xopen(fn_pac, "rb");
+
+	// prepare sequence
+	pac_size = (bwt->seq_len>>2) + ((bwt->seq_len&3) == 0? 0 : 1);
+	buf2 = (ubyte_t*)calloc(pac_size, 1);
+	err_fread_noeof(buf2, 1, pac_size, fp);
+	err_fclose(fp);
+	memset(bwt->L2, 0, 5 * 4);
+	buf = (ubyte_t*)calloc(bwt->seq_len + 1, 1);
+	for (i = 0; i < bwt->seq_len; ++i) {
+		buf[i] = buf2[i>>2] >> ((3 - (i&3)) << 1) & 3;
+		++bwt->L2[1+buf[i]];
+	}
+	for (i = 2; i <= 4; ++i) bwt->L2[i] += bwt->L2[i-1];
+	free(buf2);
+
+	// Burrows-Wheeler Transform
+	if (use_is) {
+		bwt->primary = is_bwt(buf, bwt->seq_len);
+	} else {
+		rope_t *r;
+		int64_t x;
+		rpitr_t itr;
+		const uint8_t *blk;
+
+		r = rope_init(ROPE_DEF_MAX_NODES, ROPE_DEF_BLOCK_LEN);
+		for (i = bwt->seq_len - 1, x = 0; i >= 0; --i) {
+			int c = buf[i] + 1;
+			x = rope_insert_run(r, x, c, 1, 0) + 1;
+			while (--c >= 0) x += r->c[c];
+		}
+		bwt->primary = x;
+		rope_itr_first(r, &itr);
+		x = 0;
+		while ((blk = rope_itr_next_block(&itr)) != 0) {
+			const uint8_t *q = blk + 2, *end = blk + 2 + *rle_nptr(blk);
+			while (q < end) {
+				int c = 0;
+				int64_t l;
+				rle_dec1(q, c, l);
+				for (i = 0; i < l; ++i)
+					buf[x++] = c - 1;
+			}
+		}
+		rope_destroy(r);
+	}
+	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
+	for (i = 0; i < bwt->seq_len; ++i)
+		bwt->bwt[i>>4] |= buf[i] << ((15 - (i&15)) << 1);
+	free(buf);
+	return bwt;
+}
+
+int bwa_pac2bwt(int argc, char *argv[]) // the "pac2bwt" command; IMPORTANT: bwt generated at this step CANNOT be used with BWA. bwtupdate is required!
+{
+	bwt_t *bwt;
+	int c, use_is = 1;
+	while ((c = getopt(argc, argv, "d")) >= 0) {
+		switch (c) {
+		case 'd': use_is = 0; break;
+		default: return 1;
+		}
+	}
+	if (optind + 2 > argc) {
+		fprintf(stderr, "Usage: bwa pac2bwt [-d] <in.pac> <out.bwt>\n");
+		return 1;
+	}
+	bwt = bwt_pac2bwt(argv[optind], use_is);
+	bwt_dump_bwt(argv[optind+1], bwt);
+	bwt_destroy(bwt);
+	return 0;
+}
+
+#define bwt_B00(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
+
+void bwt_bwtupdate_core(bwt_t *bwt)
+{
+	bwtint_t i, k, c[4], n_occ;
+	uint32_t *buf;
+
+	n_occ = (bwt->seq_len + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;
+	bwt->bwt_size += n_occ * sizeof(bwtint_t); // the new size
+	buf = (uint32_t*)calloc(bwt->bwt_size, 4); // will be the new bwt
+	c[0] = c[1] = c[2] = c[3] = 0;
+	for (i = k = 0; i < bwt->seq_len; ++i) {
+		if (i % OCC_INTERVAL == 0) {
+			memcpy(buf + k, c, sizeof(bwtint_t) * 4);
+			k += sizeof(bwtint_t); // in fact: sizeof(bwtint_t)=4*(sizeof(bwtint_t)/4)
+		}
+		if (i % 16 == 0) buf[k++] = bwt->bwt[i/16]; // 16 == sizeof(uint32_t)/2
+		++c[bwt_B00(bwt, i)];
+	}
+	// the last element
+	memcpy(buf + k, c, sizeof(bwtint_t) * 4);
+	xassert(k + sizeof(bwtint_t) == bwt->bwt_size, "inconsistent bwt_size");
+	// update bwt
+	free(bwt->bwt); bwt->bwt = buf;
+}
+
+int bwa_bwtupdate(int argc, char *argv[]) // the "bwtupdate" command
+{
+	bwt_t *bwt;
+	if (argc != 2) {
+		fprintf(stderr, "Usage: bwa bwtupdate <the.bwt>\n");
+		return 1;
+	}
+	bwt = bwt_restore_bwt(argv[1]);
+	bwt_bwtupdate_core(bwt);
+	bwt_dump_bwt(argv[1], bwt);
+	bwt_destroy(bwt);
+	return 0;
+}
+
+int bwa_bwt2sa(int argc, char *argv[]) // the "bwt2sa" command
+{
+	bwt_t *bwt;
+	int c, sa_intv = 32;
+	while ((c = getopt(argc, argv, "i:")) >= 0) {
+		switch (c) {
+		case 'i': sa_intv = atoi(optarg); break;
+		default: return 1;
+		}
+	}
+	if (optind + 2 > argc) {
+		fprintf(stderr, "Usage: bwa bwt2sa [-i %d] <in.bwt> <out.sa>\n", sa_intv);
+		return 1;
+	}
+	bwt = bwt_restore_bwt(argv[optind]);
+	bwt_cal_sa(bwt, sa_intv);
+	bwt_dump_sa(argv[optind+1], bwt);
+	bwt_destroy(bwt);
+	return 0;
+}
+
+int bwa_index(int argc, char *argv[]) // the "index" command
+{
+	int c, algo_type = BWTALGO_AUTO, is_64 = 0, block_size = 10000000;
+	char *prefix = 0, *str;
+	while ((c = getopt(argc, argv, "6a:p:b:")) >= 0) {
+		switch (c) {
+		case 'a': // if -a is not set, algo_type will be determined later
+			if (strcmp(optarg, "rb2") == 0) algo_type = BWTALGO_RB2;
+			else if (strcmp(optarg, "bwtsw") == 0) algo_type = BWTALGO_BWTSW;
+			else if (strcmp(optarg, "is") == 0) algo_type = BWTALGO_IS;
+			else err_fatal(__func__, "unknown algorithm: '%s'.", optarg);
+			break;
+		case 'p': prefix = strdup(optarg); break;
+		case '6': is_64 = 1; break;
+		case 'b':
+			block_size = strtol(optarg, &str, 10);
+			if (*str == 'G' || *str == 'g') block_size *= 1024 * 1024 * 1024;
+			else if (*str == 'M' || *str == 'm') block_size *= 1024 * 1024;
+			else if (*str == 'K' || *str == 'k') block_size *= 1024;
+			break;
+		default: return 1;
+		}
+	}
+
+	if (optind + 1 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa index [options] <in.fasta>\n\n");
+		fprintf(stderr, "Options: -a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]\n");
+		fprintf(stderr, "         -p STR    prefix of the index [same as fasta name]\n");
+		fprintf(stderr, "         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [%d]\n", block_size);
+		fprintf(stderr, "         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.* \n");
+		fprintf(stderr, "\n");
+		fprintf(stderr,	"Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
+		fprintf(stderr, "         `-a div' do not work not for long genomes.\n\n");
+		return 1;
+	}
+	if (prefix == 0) {
+		prefix = malloc(strlen(argv[optind]) + 4);
+		strcpy(prefix, argv[optind]);
+		if (is_64) strcat(prefix, ".64");
+	}
+	bwa_idx_build(argv[optind], prefix, algo_type, block_size);
+	free(prefix);
+	return 0;
+}
+
+int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_size)
+{
+	extern void bwa_pac_rev_core(const char *fn, const char *fn_rev);
+
+	char *str, *str2, *str3;
+	clock_t t;
+	int64_t l_pac;
+
+	str  = (char*)calloc(strlen(prefix) + 10, 1);
+	str2 = (char*)calloc(strlen(prefix) + 10, 1);
+	str3 = (char*)calloc(strlen(prefix) + 10, 1);
+
+	{ // nucleotide indexing
+		gzFile fp = xzopen(fa, "r");
+		t = clock();
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Pack FASTA... ");
+		l_pac = bns_fasta2bntseq(fp, prefix, 0);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		err_gzclose(fp);
+	}
+	if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
+	{
+		strcpy(str, prefix); strcat(str, ".pac");
+		strcpy(str2, prefix); strcat(str2, ".bwt");
+		t = clock();
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
+		if (algo_type == 2) bwt_bwtgen2(str, str2, block_size);
+		else if (algo_type == 1 || algo_type == 3) {
+			bwt_t *bwt;
+			bwt = bwt_pac2bwt(str, algo_type == 3);
+			bwt_dump_bwt(str2, bwt);
+			bwt_destroy(bwt);
+		}
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+	}
+	{
+		bwt_t *bwt;
+		strcpy(str, prefix); strcat(str, ".bwt");
+		t = clock();
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Update BWT... ");
+		bwt = bwt_restore_bwt(str);
+		bwt_bwtupdate_core(bwt);
+		bwt_dump_bwt(str, bwt);
+		bwt_destroy(bwt);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+	}
+	{
+		gzFile fp = xzopen(fa, "r");
+		t = clock();
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
+		l_pac = bns_fasta2bntseq(fp, prefix, 1);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+		err_gzclose(fp);
+	}
+	{
+		bwt_t *bwt;
+		strcpy(str, prefix); strcat(str, ".bwt");
+		strcpy(str3, prefix); strcat(str3, ".sa");
+		t = clock();
+		if (bwa_verbose >= 3) fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
+		bwt = bwt_restore_bwt(str);
+		bwt_cal_sa(bwt, 32);
+		bwt_dump_sa(str3, bwt);
+		bwt_destroy(bwt);
+		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+	}
+	free(str3); free(str2); free(str);
+	return 0;
+}

bwtsw2.h

@@ -0,0 +1,69 @@
+#ifndef LH3_BWTSW2_H
+#define LH3_BWTSW2_H
+
+#include <stdint.h>
+#include "bntseq.h"
+#include "bwt_lite.h"
+#include "bwt.h"
+
+#define BSW2_FLAG_MATESW  0x100
+#define BSW2_FLAG_TANDEM  0x200
+#define BSW2_FLAG_MOVED   0x400
+#define BSW2_FLAG_RESCUED 0x800
+
+typedef struct {
+	int skip_sw:8, cpy_cmt:8, hard_clip:16;
+	int a, b, q, r, t, qr, bw, max_ins, max_chain_gap;
+	int z, is, t_seeds, multi_2nd;
+	float mask_level, coef;
+	int n_threads, chunk_size;
+} bsw2opt_t;
+
+typedef struct {
+	bwtint_t k, l;
+	uint32_t flag:18, n_seeds:13, is_rev:1;
+	int len, G, G2;
+	int beg, end;
+} bsw2hit_t;
+
+typedef struct {
+	int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
+	uint32_t *cigar;
+} bsw2aux_t;
+
+typedef struct {
+	int n, max;
+	bsw2hit_t *hits;
+	bsw2aux_t *aux;
+} bwtsw2_t;
+
+typedef struct {
+	void *stack;
+	int max_l;
+	uint8_t *aln_mem;
+} bsw2global_t;
+
+typedef struct {
+	int l, tid;
+	char *name, *seq, *qual, *sam, *comment;
+} bsw2seq1_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bsw2opt_t *bsw2_init_opt();
+	bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
+	void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2);
+	void bsw2_destroy(bwtsw2_t *b);
+
+	bsw2global_t *bsw2_global_init();
+	void bsw2_global_destroy(bsw2global_t *_pool);
+
+	void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwtsw2_aux.c

@@ -0,0 +1,776 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+#ifdef HAVE_PTHREAD
+#include <pthread.h>
+#endif
+#include "bntseq.h"
+#include "bwt_lite.h"
+#include "utils.h"
+#include "bwtsw2.h"
+#include "kstring.h"
+#include "bwa.h"
+#include "ksw.h"
+
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+#include "ksort.h"
+#define __left_lt(a, b) ((a).end > (b).end)
+KSORT_INIT(hit, bsw2hit_t, __left_lt)
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+
+extern unsigned char nst_nt4_table[256];
+
+unsigned char nt_comp_table[256] = {
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
+	'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
+	'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n',
+	'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
+};
+
+extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
+extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level);
+
+bsw2opt_t *bsw2_init_opt()
+{
+	bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
+	o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
+	o->bw = 50;
+	o->max_ins = 20000;
+	o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0; o->skip_sw = 0;
+	o->mask_level = 0.50f; o->coef = 5.5f;
+	o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
+	o->max_chain_gap = 10000;
+	o->cpy_cmt = 0;
+	return o;
+}
+
+void bsw2_destroy(bwtsw2_t *b)
+{
+	int i;
+	if (b == 0) return;
+	if (b->aux)
+		for (i = 0; i < b->n; ++i) free(b->aux[i].cigar);
+	free(b->aux); free(b->hits);
+	free(b);
+}
+
+bwtsw2_t *bsw2_dup_no_cigar(const bwtsw2_t *b)
+{
+	bwtsw2_t *p;
+	p = calloc(1, sizeof(bwtsw2_t));
+	p->max = p->n = b->n;
+	if (b->n) {
+		kroundup32(p->max);
+		p->hits = calloc(p->max, sizeof(bsw2hit_t));
+		memcpy(p->hits, b->hits, p->n * sizeof(bsw2hit_t));
+	}
+	return p;
+}
+
+#define __gen_ap(par, opt) do {									\
+		int i;													\
+		for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b;	\
+		for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \
+		(par).gap_open = (opt)->q; (par).gap_ext = (opt)->r;	\
+		(par).gap_end = (opt)->r;								\
+		(par).row = 5; (par).band_width = opt->bw;				\
+	} while (0)
+
+void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
+{
+	int i;
+	bwtint_t k;
+	uint8_t *target = 0, *query;
+	int8_t mat[25];
+
+	bwa_fill_scmat(opt->a, opt->b, mat);
+	query = calloc(lq, 1);
+	// sort according to the descending order of query end
+	ks_introsort(hit, b->n, b->hits);
+	target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
+	// reverse _query
+	for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
+	// core loop
+	for (i = 0; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
+		int score, j, qle, tle;
+		p->n_seeds = 1;
+		if (p->l || p->k == 0) continue;
+		for (j = score = 0; j < i; ++j) {
+			bsw2hit_t *q = b->hits + j;
+			if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
+				if (q->n_seeds < (1<<13) - 2) ++q->n_seeds;
+				++score;
+			}
+		}
+		if (score) continue;
+		if (lt > p->k) lt = p->k;
+		for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
+			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
+		lt = j;
+		score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, p->G, &qle, &tle, 0, 0, 0);
+		if (score > p->G) { // extensible
+			p->G = score;
+			p->k -= tle;
+			p->len += tle;
+			p->beg -= qle;
+		}
+	}
+	free(query); free(target);
+}
+
+void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
+{
+	int i;
+	bwtint_t k;
+	uint8_t *target;
+	int8_t mat[25];
+
+	bwa_fill_scmat(opt->a, opt->b, mat);
+	target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
+	for (i = 0; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
+		int j, score, qle, tle;
+		if (p->l) continue;
+		for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
+			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
+		lt = j;
+		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, 1, &qle, &tle, 0, 0, 0) - 1;
+//		if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
+		if (score >= p->G) {
+			p->G = score;
+			p->len = tle;
+			p->end = p->beg + qle;
+		}
+	}
+	free(target);
+}
+
+/* generate CIGAR array(s) in b->cigar[] */
+static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], int64_t l_pac, const uint8_t *pac, bwtsw2_t *b, const char *name)
+{
+	int i;
+	int8_t mat[25];
+
+	bwa_fill_scmat(opt->a, opt->b, mat);
+	for (i = 0; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		bsw2aux_t *q = b->aux + i;
+		uint8_t *query;
+		int beg, end, score;
+		if (p->l) continue;
+		beg = (p->flag & 0x10)? lq - p->end : p->beg;
+		end = (p->flag & 0x10)? lq - p->beg : p->end;
+		query = seq[(p->flag & 0x10)? 1 : 0] + beg;
+		q->cigar = bwa_gen_cigar(mat, opt->q, opt->r, opt->bw, l_pac, pac, end - beg, query, p->k, p->k + p->len, &score, &q->n_cigar, &q->nm);
+#if 0
+		if (name && score != p->G) { // debugging only
+			int j, glen = 0;
+			for (j = 0; j < q->n_cigar; ++j)
+				if ((q->cigar[j]&0xf) == 1 || (q->cigar[j]&0xf) == 2)
+					glen += q->cigar[j]>>4;
+			fprintf(stderr, "[E::%s] %s - unequal score: %d != %d; (qlen, aqlen, arlen, glen, bw) = (%d, %d, %d, %d, %d)\n",
+					__func__, name, score, p->G, lq, end - beg, p->len, glen, opt->bw);
+		}
+#endif
+		if (q->cigar && (beg != 0 || end < lq)) { // write soft clipping
+			q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
+			if (beg != 0) {
+				memmove(q->cigar + 1, q->cigar, q->n_cigar * 4);
+				q->cigar[0] = beg<<4 | 4;
+				++q->n_cigar;
+			}
+			if (end < lq) {
+				q->cigar[q->n_cigar] = (lq - end)<<4 | 4;
+				++q->n_cigar;
+			}
+		}
+	}
+}
+
+/* this is for the debugging purpose only */
+void bsw2_debug_hits(const bwtsw2_t *b)
+{
+	int i;
+	printf("# raw hits: %d\n", b->n);
+	for (i = 0; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		if (p->G > 0)
+			printf("G=%d, G2=%d, len=%d, [%d,%d), k=%lu, l=%lu, #seeds=%d, is_rev=%d\n", p->G, p->G2, p->len, p->beg, p->end, (long)p->k, (long)p->l, p->n_seeds, p->is_rev);
+	}
+}
+
+static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse)
+{
+	int i;
+	if (b[0]->n + b[1]->n > b[0]->max) {
+		b[0]->max = b[0]->n + b[1]->n;
+		b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t));
+	}
+	for (i = 0; i < b[1]->n; ++i) {
+		bsw2hit_t *p = b[0]->hits + b[0]->n + i;
+		*p = b[1]->hits[i];
+		if (is_reverse) {
+			int x = p->beg;
+			p->beg = l - p->end;
+			p->end = l - x;
+			p->flag |= 0x10;
+		}
+	}
+	b[0]->n += b[1]->n;
+	bsw2_destroy(b[1]);
+	b[1] = 0;
+}
+/* seq[0] is the forward sequence and seq[1] is the reverse complement. */
+static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target,
+								int l, uint8_t *seq[2], bsw2global_t *pool)
+{
+	extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]);
+	bwtsw2_t *b[2], **bb[2], **_b, *p;
+	int k, j;
+	bwtl_t *query;
+	query = bwtl_seq2bwtl(l, seq[0]);
+	_b = bsw2_core(bns, opt, query, target, pool);
+	bwtl_destroy(query);
+	for (k = 0; k < 2; ++k) {
+		bb[k] = calloc(2, sizeof(void*));
+		bb[k][0] = calloc(1, sizeof(bwtsw2_t));
+		bb[k][1] = calloc(1, sizeof(bwtsw2_t));
+	}
+	for (k = 0; k < 2; ++k) { // separate _b into bb[2] based on the strand
+		for (j = 0; j < _b[k]->n; ++j) {
+			bsw2hit_t *q;
+			p = bb[_b[k]->hits[j].is_rev][k];
+			if (p->n == p->max) {
+				p->max = p->max? p->max<<1 : 8;
+				p->hits = realloc(p->hits, p->max * sizeof(bsw2hit_t));
+			}
+			q = &p->hits[p->n++];
+			*q = _b[k]->hits[j];
+			if (_b[k]->hits[j].is_rev) {
+				int x = q->beg;
+				q->beg = l - q->end;
+				q->end = l - x;
+			}
+		}
+	}
+	b[0] = bb[0][1]; b[1] = bb[1][1]; // bb[*][1] are "narrow SA hits"
+	bsw2_chain_filter(opt, l, b); // NB: only unique seeds are chained
+	for (k = 0; k < 2; ++k) {
+		bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, pool->aln_mem);
+		merge_hits(bb[k], l, 0); // bb[k][1] is merged to bb[k][0] here
+		bsw2_resolve_duphits(0, 0, bb[k][0], 0);
+		bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, pool->aln_mem);
+		bsw2_resolve_duphits(0, 0, bb[k][0], 0);
+		b[k] = bb[k][0];
+		free(bb[k]);		
+	}
+	merge_hits(b, l, 1); // again, b[1] is merged to b[0]
+	bsw2_resolve_query_overlaps(b[0], opt->mask_level);
+	bsw2_destroy(_b[0]); bsw2_destroy(_b[1]); free(_b);
+	return b[0];
+}
+
+/* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */
+static void flag_fr(bwtsw2_t *b[2])
+{
+	int i, j;
+	for (i = 0; i < b[0]->n; ++i) {
+		bsw2hit_t *p = b[0]->hits + i;
+		p->flag |= 0x10000;
+	}
+	for (i = 0; i < b[1]->n; ++i) {
+		bsw2hit_t *p = b[1]->hits + i;
+		p->flag |= 0x20000;
+	}
+	for (i = 0; i < b[0]->n; ++i) {
+		bsw2hit_t *p = b[0]->hits + i;
+		for (j = 0; j < b[1]->n; ++j) {
+			bsw2hit_t *q = b[1]->hits + j;
+			if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
+				q->flag |= 0x30000; p->flag |= 0x30000;
+				break;
+			}
+		}
+	}
+}
+
+typedef struct {
+	int n, max;
+	bsw2seq1_t *seq;
+} bsw2seq_t;
+
+static int fix_cigar(const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
+{
+	// FIXME: this routine does not work if the query bridge three reference sequences
+	int32_t coor, refl, lq;
+	int x, y, i, seqid;
+	bns_cnt_ambi(bns, p->k, p->len, &seqid);
+	coor = p->k - bns->anns[seqid].offset;
+	refl = bns->anns[seqid].len;
+	x = coor; y = 0;
+	// test if the alignment goes beyond the boundary
+	for (i = 0; i < n_cigar; ++i) {
+		int op = cigar[i]&0xf, ln = cigar[i]>>4;
+		if (op == 1 || op == 4 || op == 5) y += ln;
+		else if (op == 2) x += ln;
+		else x += ln, y += ln;
+	}
+	lq = y; // length of the query sequence
+	if (x > refl) { // then fix it
+		int j, nc, mq[2], nlen[2];
+		uint32_t *cn;
+		bwtint_t kk = 0;
+		nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0;
+		cn = calloc(n_cigar + 3, 4);
+		x = coor; y = 0;
+		for (i = j = 0; i < n_cigar; ++i) {
+			int op = cigar[i]&0xf, ln = cigar[i]>>4;
+			if (op == 4 || op == 5 || op == 1) { // ins or clipping
+				y += ln;
+				cn[j++] = cigar[i];
+			} else if (op == 2) { // del
+				if (x + ln >= refl && nc == 0) {
+					cn[j++] = (uint32_t)(lq - y)<<4 | 4;
+					nc = j;
+					cn[j++] = (uint32_t)y<<4 | 4;
+					kk = p->k + (x + ln - refl);
+					nlen[0] = x - coor;
+					nlen[1] = p->len - nlen[0] - ln;
+				} else cn[j++] = cigar[i];
+				x += ln;
+			} else if (op == 0) { // match
+				if (x + ln >= refl && nc == 0) {
+					// FIXME: not consider a special case where a split right between M and I
+					cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M
+					cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S
+					nc = j;
+					mq[0] += refl - x;
+					cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4;
+					if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0;
+					mq[1] += x + ln - refl;
+					kk = bns->anns[seqid].offset + refl;
+					nlen[0] = refl - coor;
+					nlen[1] = p->len - nlen[0];
+				} else {
+					cn[j++] = cigar[i];
+					mq[nc?1:0] += ln;
+				}
+				x += ln; y += ln;
+			}
+		}
+		if (mq[0] > mq[1]) { // then take the first alignment
+			n_cigar = nc;
+			memcpy(cigar, cn, 4 * nc);
+			p->len = nlen[0];
+		} else {
+			p->k = kk; p->len = nlen[1];
+			n_cigar = j - nc;
+			memcpy(cigar, cn + nc, 4 * (j - nc));
+		}
+		free(cn);
+	}
+	return n_cigar;
+}
+
+static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b, const char *name)
+{
+	int i;
+	// allocate for b->aux
+	if (b->n<<1 < b->max) {
+		b->max = b->n;
+		kroundup32(b->max);
+		b->hits = realloc(b->hits, b->max * sizeof(bsw2hit_t));
+	}
+	b->aux = calloc(b->n, sizeof(bsw2aux_t));
+	// generate CIGAR
+	gen_cigar(opt, qlen, seq, bns->l_pac, pac, b, name);
+	// fix CIGAR, generate mapQ, and write chromosomal position
+	for (i = 0; i < b->n; ++i) {
+		bsw2hit_t *p = &b->hits[i];
+		bsw2aux_t *q = &b->aux[i];
+		q->flag = p->flag & 0xfe;
+		q->isize = 0;
+		if (p->l == 0) { // unique hit
+			float c = 1.0;
+			int subo;
+			// fix out-of-boundary CIGAR
+			q->n_cigar = fix_cigar(bns, p, q->n_cigar, q->cigar);
+			// compute mapQ
+			subo = p->G2 > opt->t? p->G2 : opt->t;
+			if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
+			if (p->n_seeds < 2) c *= .2;
+			q->qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499);
+			if (q->qual > 250) q->qual = 250;
+			if (q->qual < 0) q->qual = 0;
+			if (p->flag&1) q->qual = 0; // this is a random hit
+			q->pqual = q->qual; // set the paired qual as qual
+			// get the chromosomal position
+			q->nn = bns_cnt_ambi(bns, p->k, p->len, &q->chr);
+			q->pos = p->k - bns->anns[q->chr].offset;
+		} else q->qual = 0, q->n_cigar = 0, q->chr = q->pos = -1, q->nn = 0;
+	}
+}
+
+static void update_mate_aux(bwtsw2_t *b, const bwtsw2_t *m)
+{
+	int i;
+	if (m == 0) return;
+	// update flag, mchr and mpos
+	for (i = 0; i < b->n; ++i) {
+		bsw2aux_t *q = &b->aux[i];
+		q->flag |= 1; // paired
+		if (m->n == 0) q->flag |= 8; // mate unmapped
+		if (m->n == 1) {
+			q->mchr = m->aux[0].chr;
+			q->mpos = m->aux[0].pos;
+			if (m->aux[0].flag&0x10) q->flag |= 0x20; // mate reverse strand
+			if (q->chr == q->mchr) { // set insert size
+				if (q->mpos + m->hits[0].len > q->pos)
+					q->isize = q->mpos + m->hits[0].len - q->pos;
+				else q->isize = q->mpos - q->pos - b->hits[0].len;
+			} else q->isize = 0;
+		} else q->mchr = q->mpos = -1;
+	}
+	// update mapping quality
+	if (b->n == 1 && m->n == 1) {
+		bsw2hit_t *p = &b->hits[0];
+		if (p->flag & BSW2_FLAG_MATESW) { // this alignment is found by Smith-Waterman
+			if (!(p->flag & BSW2_FLAG_TANDEM) && b->aux[0].pqual < 20)
+				b->aux[0].pqual = 20;
+			if (b->aux[0].pqual >= m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
+		} else if ((p->flag & 2) && !(m->hits[0].flag & BSW2_FLAG_MATESW)) { // properly paired
+			if (!(p->flag & BSW2_FLAG_TANDEM)) { // pqual is bounded by [b->aux[0].qual,m->aux[0].qual]
+				b->aux[0].pqual += 20;
+				if (b->aux[0].pqual > m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
+				if (b->aux[0].pqual < b->aux[0].qual) b->aux[0].pqual = b->aux[0].qual;
+			}
+		}
+	}
+}
+
+/* generate SAM lines for a sequence in ks with alignment stored in
+ * b. ks->name and ks->seq will be freed and set to NULL in the end. */
+static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b, int is_pe, bwtsw2_t *bmate)
+{
+	int i, k;
+	kstring_t str;
+	memset(&str, 0, sizeof(kstring_t));
+	if (b == 0 || b->n == 0) { // no hits
+		ksprintf(&str, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t", ks->name);
+		for (i = 0; i < ks->l; ++i) kputc(ks->seq[i], &str);
+		if (ks->qual) {
+			kputc('\t', &str);
+			for (i = 0; i < ks->l; ++i) kputc(ks->qual[i], &str);
+		} else kputs("\t*", &str);
+		kputc('\n', &str);
+	}
+	for (i = 0; b && i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		bsw2aux_t *q = b->aux + i;
+		int j, beg, end, type = 0;
+		// print mandatory fields before SEQ
+		if (q->cigar == 0) q->flag |= 0x4;
+		ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
+		ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
+		if (p->l == 0 && q->cigar) { // not a repetitive hit
+			ksprintf(&str, "\t%d\t", q->pqual);
+			for (k = 0; k < q->n_cigar; ++k)
+				ksprintf(&str, "%d%c", q->cigar[k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[q->cigar[k]&0xf]);
+		} else ksprintf(&str, "\t0\t*");
+		if (!is_pe) kputs("\t*\t0\t0\t", &str);
+		else ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
+		// get the sequence begin and end
+		beg = 0; end = ks->l;
+		if (opt->hard_clip && q->cigar) {
+			if ((q->cigar[0]&0xf) == 4) beg += q->cigar[0]>>4;
+			if ((q->cigar[q->n_cigar-1]&0xf) == 4) end -= q->cigar[q->n_cigar-1]>>4;
+		}
+		for (j = beg; j < end; ++j) {
+			if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str);
+			else kputc(ks->seq[j], &str);
+		}
+		// print base quality if present
+		if (ks->qual) {
+			kputc('\t', &str);
+			for (j = beg; j < end; ++j) {
+				if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str);
+				else kputc(ks->qual[j], &str);
+			}
+		} else kputs("\t*", &str);
+		// print optional tags
+		ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tNM:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, q->nm);
+		if (q->nn) ksprintf(&str, "\tXN:i:%d", q->nn);
+		if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
+		if (p->flag&BSW2_FLAG_MATESW) type |= 1;
+		if (p->flag&BSW2_FLAG_TANDEM) type |= 2;
+		if (type) ksprintf(&str, "\tXT:i:%d", type);
+		if (opt->cpy_cmt && ks->comment) {
+			int l = strlen(ks->comment);
+			if (l >= 6 && ks->comment[2] == ':' && ks->comment[4] == ':') {
+				kputc('\t', &str); kputs(ks->comment, &str);
+			}
+		}
+		kputc('\n', &str);
+	}
+	ks->sam = str.s;
+	free(ks->seq); ks->seq = 0;
+	free(ks->qual); ks->qual = 0;
+	free(ks->name); ks->name = 0;
+}
+
+static void update_opt(bsw2opt_t *dst, const bsw2opt_t *src, int qlen)
+{
+	double ll = log(qlen);
+	int i, k;
+	*dst = *src;
+	if (dst->t < ll * dst->coef) dst->t = (int)(ll * dst->coef + .499);
+	// set band width: the query length sets a boundary on the maximum band width
+	k = (qlen * dst->a - 2 * dst->q) / (2 * dst->r + dst->a);
+	i = (qlen * dst->a - dst->a - dst->t) / dst->r;
+	if (k > i) k = i;
+	if (k < 1) k = 1; // I do not know if k==0 causes troubles
+	dst->bw = src->bw < k? src->bw : k;
+}
+
+/* Core routine to align reads in _seq. It is separated from
+ * process_seqs() to realize multi-threading */ 
+static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
+{
+	int x;
+	bsw2opt_t opt;
+	bsw2global_t *pool = bsw2_global_init();
+	bwtsw2_t **buf;
+	buf = calloc(_seq->n, sizeof(void*));
+	for (x = 0; x < _seq->n; ++x) {
+		bsw2seq1_t *p = _seq->seq + x;
+		uint8_t *seq[2], *rseq[2];
+		int i, l, k;
+		bwtsw2_t *b[2];
+		l = p->l;
+		update_opt(&opt, _opt, p->l);
+		if (pool->max_l < l) { // then enlarge working space for aln_extend_core()
+			int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l;
+			pool->max_l = l;
+			pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24);
+		}
+		// set seq[2] and rseq[2]
+		seq[0] = calloc(l * 4, 1);
+		seq[1] = seq[0] + l;
+		rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l;
+		// convert sequences to 2-bit representation
+		for (i = k = 0; i < l; ++i) {
+			int c = nst_nt4_table[(int)p->seq[i]];
+			if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled
+			seq[0][i] = c;
+			seq[1][l-1-i] = 3 - c;
+			rseq[0][l-1-i] = 3 - c;
+			rseq[1][i] = c;
+		}
+		if (l - k < opt.t) { // too few unambiguous bases
+			buf[x] = calloc(1, sizeof(bwtsw2_t));
+			free(seq[0]); continue;
+		}
+		// alignment
+		b[0] = bsw2_aln1_core(&opt, bns, pac, target, l, seq, pool);
+		for (k = 0; k < b[0]->n; ++k)
+			if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
+		if (k < b[0]->n) {
+			b[1] = bsw2_aln1_core(&opt, bns, pac, target, l, rseq, pool);
+			for (i = 0; i < b[1]->n; ++i) {
+				bsw2hit_t *p = &b[1]->hits[i];
+				int x = p->beg;
+				p->flag ^= 0x10, p->is_rev ^= 1; // flip the strand
+				p->beg = l - p->end;
+				p->end = l - x;
+			}
+			flag_fr(b);
+			merge_hits(b, l, 0);
+			bsw2_resolve_duphits(0, 0, b[0], 0);
+			bsw2_resolve_query_overlaps(b[0], opt.mask_level);
+		} else b[1] = 0;
+		// generate CIGAR and print SAM
+		buf[x] = bsw2_dup_no_cigar(b[0]);
+		// free
+		free(seq[0]);
+		bsw2_destroy(b[0]);
+	}
+	if (is_pe) bsw2_pair(&opt, bns->l_pac, pac, _seq->n, _seq->seq, buf);
+	for (x = 0; x < _seq->n; ++x) {
+		bsw2seq1_t *p = _seq->seq + x;
+		uint8_t *seq[2];
+		int i;
+		seq[0] = malloc(p->l * 2); seq[1] = seq[0] + p->l;
+		for (i = 0; i < p->l; ++i) {
+			int c = nst_nt4_table[(int)p->seq[i]];
+			if (c >= 4) c = (int)(drand48() * 4);
+			seq[0][i] = c;
+			seq[1][p->l-1-i] = 3 - c;
+		}
+		update_opt(&opt, _opt, p->l);
+		write_aux(&opt, bns, p->l, seq, pac, buf[x], _seq->seq[x].name);
+		free(seq[0]);
+	}
+	for (x = 0; x < _seq->n; ++x) {
+		if (is_pe) update_mate_aux(buf[x], buf[x^1]);
+		print_hits(bns, &opt, &_seq->seq[x], buf[x], is_pe, buf[x^1]);
+	}
+	for (x = 0; x < _seq->n; ++x) bsw2_destroy(buf[x]);
+	free(buf);
+	bsw2_global_destroy(pool);
+}
+
+#ifdef HAVE_PTHREAD
+typedef struct {
+	int tid, is_pe;
+	bsw2seq_t *_seq;
+	const bsw2opt_t *_opt;
+	const bntseq_t *bns;
+	uint8_t *pac;
+	const bwt_t *target;
+} thread_aux_t;
+
+/* another interface to bsw2_aln_core() to facilitate pthread_create() */
+static void *worker(void *data)
+{
+	thread_aux_t *p = (thread_aux_t*)data;
+	bsw2_aln_core(p->_seq, p->_opt, p->bns, p->pac, p->target, p->is_pe);
+	return 0;
+}
+#endif
+
+/* process sequences stored in _seq, generate SAM lines for these
+ * sequences and reset _seq afterwards. */
+static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
+{
+	int i;
+	is_pe = is_pe? 1 : 0;
+
+#ifdef HAVE_PTHREAD
+	if (opt->n_threads <= 1) {
+		bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
+	} else {
+		pthread_t *tid;
+		pthread_attr_t attr;
+		thread_aux_t *data;
+		int j;
+		pthread_attr_init(&attr);
+		pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+		data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
+		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
+		for (j = 0; j < opt->n_threads; ++j) {
+			thread_aux_t *p = data + j;
+			p->tid = j; p->_opt = opt; p->bns = bns; p->is_pe = is_pe;
+			p->pac = pac; p->target = target;
+			p->_seq = calloc(1, sizeof(bsw2seq_t));
+			p->_seq->max = (_seq->n + opt->n_threads - 1) / opt->n_threads + 1;
+			p->_seq->n = 0;
+			p->_seq->seq = calloc(p->_seq->max, sizeof(bsw2seq1_t));
+		}
+		for (i = 0; i < _seq->n; ++i) { // assign sequences to each thread
+			bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
+			p->seq[p->n++] = _seq->seq[i];
+		}
+		for (j = 0; j < opt->n_threads; ++j) pthread_create(&tid[j], &attr, worker, &data[j]);
+		for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
+		for (j = 0; j < opt->n_threads; ++j) data[j]._seq->n = 0;
+		for (i = 0; i < _seq->n; ++i) { // copy the result from each thread back
+			bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
+			_seq->seq[i] = p->seq[p->n++];
+		}
+		for (j = 0; j < opt->n_threads; ++j) {
+			thread_aux_t *p = data + j;
+			free(p->_seq->seq);
+			free(p->_seq);
+		}
+		free(data); free(tid);
+	}
+#else
+	bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
+#endif
+
+	// print and reset
+	for (i = 0; i < _seq->n; ++i) {
+		bsw2seq1_t *p = _seq->seq + i;
+		if (p->sam) err_printf("%s", p->sam);
+		free(p->name); free(p->seq); free(p->qual); free(p->sam);
+		p->tid = -1; p->l = 0;
+		p->name = p->seq = p->qual = p->sam = 0;
+	}
+	err_fflush(stdout);
+	_seq->n = 0;
+}
+
+void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2)
+{
+	gzFile fp, fp2;
+	kseq_t *ks, *ks2;
+	int l, is_pe = 0, i, n;
+	uint8_t *pac;
+	bsw2seq_t *_seq;
+	bseq1_t *bseq;
+
+	pac = calloc(bns->l_pac/4+1, 1);
+	for (l = 0; l < bns->n_seqs; ++l)
+		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
+	err_fread_noeof(pac, 1, bns->l_pac/4+1, bns->fp_pac);
+	fp = xzopen(fn, "r");
+	ks = kseq_init(fp);
+	_seq = calloc(1, sizeof(bsw2seq_t));
+	if (fn2) {
+		fp2 = xzopen(fn2, "r");
+		ks2 = kseq_init(fp2);
+		is_pe = 1;
+	} else fp2 = 0, ks2 = 0, is_pe = 0;
+	while ((bseq = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
+		int size = 0;
+		if (n > _seq->max) {
+			_seq->max = n;
+			kroundup32(_seq->max);
+			_seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
+		}
+		_seq->n = n;
+		for (i = 0; i < n; ++i) {
+			bseq1_t *b = &bseq[i];
+			bsw2seq1_t *p = &_seq->seq[i];
+			p->tid = -1; p->l = b->l_seq;
+			p->name = b->name; p->seq = b->seq; p->qual = b->qual; p->comment = b->comment; p->sam = 0;
+			size += p->l;
+		}
+		fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp) ...\n", n, size);
+		free(bseq);
+		process_seqs(_seq, opt, bns, pac, target, is_pe);
+	}
+	// free
+	free(pac);
+	free(_seq->seq); free(_seq);
+	kseq_destroy(ks);
+	err_gzclose(fp);
+	if (fn2) {
+		kseq_destroy(ks2);
+		err_gzclose(fp2);
+	}
+}

bwtsw2_chain.c

@@ -0,0 +1,112 @@
+#include <stdio.h>
+#include "bwtsw2.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef struct {
+	uint32_t tbeg, tend;
+	int qbeg, qend;
+	uint32_t flag:1, idx:31;
+	int chain; // also reuse as a counter
+} hsaip_t;
+
+#define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)
+
+#include "ksort.h"
+KSORT_INIT(hsaip, hsaip_t, _hsaip_lt)
+
+static int chaining(const bsw2opt_t *opt, int shift, int n, hsaip_t *z, hsaip_t *chain)
+{
+	int j, k, m = 0;
+	ks_introsort(hsaip, n, z);
+	for (j = 0; j < n; ++j) {
+		hsaip_t *p = z + j;
+		for (k = m - 1; k >= 0; --k) {
+			hsaip_t *q = chain + k;
+			int x = p->qbeg - q->qbeg; // always positive
+			int y = p->tbeg - q->tbeg;
+			if (y > 0 && x < opt->max_chain_gap && y < opt->max_chain_gap && x - y <= opt->bw && y - x <= opt->bw) { // chained
+				if (p->qend > q->qend) q->qend = p->qend;
+				if (p->tend > q->tend) q->tend = p->tend;
+				++q->chain;
+				p->chain = shift + k;
+				break;
+			} else if (q->chain > opt->t_seeds * 2) k = 0; // if the chain is strong enough, do not check the previous chains
+		}
+		if (k < 0) { // not added to any previous chains
+			chain[m] = *p;
+			chain[m].chain = 1;
+			chain[m].idx = p->chain = shift + m;
+			++m;
+		}
+	}
+	return m;
+}
+
+void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2])
+{
+	hsaip_t *z[2], *chain[2];
+	int i, j, k, n[2], m[2], thres = opt->t_seeds * 2;
+	char *flag;
+	// initialization
+	n[0] = b[0]->n; n[1] = b[1]->n;
+	z[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
+	z[1] = z[0] + n[0];
+	chain[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
+	for (k = j = 0; k < 2; ++k) {
+		for (i = 0; i < b[k]->n; ++i) {
+			bsw2hit_t *p = b[k]->hits + i;
+			hsaip_t *q = z[k] + i;
+			q->flag = k; q->idx = i;
+			q->tbeg = p->k; q->tend = p->k + p->len;
+			q->chain = -1;
+			q->qbeg = p->beg; q->qend = p->end;
+		}
+	}
+	// chaining
+	m[0] = chaining(opt, 0,    n[0], z[0], chain[0]);
+	chain[1] = chain[0] + m[0];
+	m[1] = chaining(opt, m[0], n[1], z[1], chain[1]);	
+	// change query coordinate on the reverse strand
+	for (k = 0; k < m[1]; ++k) {
+		hsaip_t *p = chain[1] + k;
+		int tmp = p->qbeg;
+		p->qbeg = len - p->qend; p->qend = len - tmp;
+	}
+	//for (k = 0; k < m[0]; ++k) printf("%d, [%d,%d), [%d,%d)\n", chain[0][k].chain, chain[0][k].tbeg, chain[0][k].tend, chain[0][k].qbeg, chain[0][k].qend);
+	// filtering
+	flag = calloc(m[0] + m[1], 1);
+	ks_introsort(hsaip, m[0] + m[1], chain[0]);
+	for (k = 1; k < m[0] + m[1]; ++k) {
+		hsaip_t *p = chain[0] + k;
+		for (j = 0; j < k; ++j) {
+			hsaip_t *q = chain[0] + j;
+			if (flag[q->idx]) continue;
+			if (q->qend >= p->qend && q->chain > p->chain * thres && p->chain < thres) {
+				flag[p->idx] = 1;
+				break;
+			}
+		}
+	}
+	for (k = 0; k < n[0] + n[1]; ++k) {
+		hsaip_t *p = z[0] + k;
+		if (flag[p->chain])
+			b[p->flag]->hits[p->idx].G = 0;
+	}
+	free(flag);
+	// squeeze out filtered elements in b[2]
+	for (k = 0; k < 2; ++k) {
+		for (j = i = 0; j < n[k]; ++j) {
+			bsw2hit_t *p = b[k]->hits + j;
+			if (p->G) {
+				if (i != j) b[k]->hits[i++] = *p;
+				else ++i;
+			}
+		}
+		b[k]->n = i;
+	}
+	// free
+	free(z[0]); free(chain[0]);
+}

bwtsw2_core.c

@@ -0,0 +1,619 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <sys/resource.h>
+#include <assert.h>
+#include "bwt_lite.h"
+#include "bwtsw2.h"
+#include "bwt.h"
+#include "kvec.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef struct {
+	bwtint_t k, l;
+} qintv_t;
+
+#define qintv_eq(a, b) ((a).k == (b).k && (a).l == (b).l)
+#define qintv_hash(a) ((a).k>>7^(a).l<<17)
+
+#include "khash.h"
+KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
+KHASH_MAP_INIT_INT64(64, uint64_t)
+
+#define MINUS_INF -0x3fffffff
+#define MASK_LEVEL 0.90f
+
+struct __mempool_t;
+static void mp_destroy(struct __mempool_t*);
+typedef struct {
+	bwtint_t qk, ql;
+	int I, D, G;
+	uint32_t pj:2, qlen:30;
+	int tlen;
+	int ppos, upos;
+	int cpos[4];
+} bsw2cell_t;
+
+#include "ksort.h"
+KSORT_INIT_GENERIC(int)
+#define __hitG_lt(a, b) (((a).G + ((int)(a).n_seeds<<2)) > (b).G + ((int)(b).n_seeds<<2))
+KSORT_INIT(hitG, bsw2hit_t, __hitG_lt)
+
+static const bsw2cell_t g_default_cell = { 0, 0, MINUS_INF, MINUS_INF, MINUS_INF, 0, 0, 0, -1, -1, {-1, -1, -1, -1} };
+
+typedef struct {
+	int n, max;
+	uint32_t tk, tl; // this is fine
+	bsw2cell_t *array;
+} bsw2entry_t, *bsw2entry_p;
+
+/* --- BEGIN: Stack operations --- */
+typedef struct {
+	int n_pending;
+	kvec_t(bsw2entry_p) stack0, pending;
+	struct __mempool_t *pool;
+} bsw2stack_t;
+
+#define stack_isempty(s) (kv_size(s->stack0) == 0 && s->n_pending == 0)
+static void stack_destroy(bsw2stack_t *s) { mp_destroy(s->pool); kv_destroy(s->stack0); kv_destroy(s->pending); free(s); }
+inline static void stack_push0(bsw2stack_t *s, bsw2entry_p e) { kv_push(bsw2entry_p, s->stack0, e); }
+inline static bsw2entry_p stack_pop(bsw2stack_t *s)
+{
+	assert(!(kv_size(s->stack0) == 0 && s->n_pending != 0));
+	return kv_pop(s->stack0);
+}
+/* --- END: Stack operations --- */
+
+/* --- BEGIN: memory pool --- */
+typedef struct __mempool_t {
+	int cnt; // if cnt!=0, then there must be memory leak
+	kvec_t(bsw2entry_p) pool;
+} mempool_t;
+inline static bsw2entry_p mp_alloc(mempool_t *mp)
+{
+	++mp->cnt;
+	if (kv_size(mp->pool) == 0) return (bsw2entry_t*)calloc(1, sizeof(bsw2entry_t));
+	else return kv_pop(mp->pool);
+}
+inline static void mp_free(mempool_t *mp, bsw2entry_p e)
+{
+	--mp->cnt; e->n = 0;
+	kv_push(bsw2entry_p, mp->pool, e);
+}
+static void mp_destroy(struct __mempool_t *mp)
+{
+	int i;
+	for (i = 0; i != kv_size(mp->pool); ++i) {
+		free(kv_A(mp->pool, i)->array);
+		free(kv_A(mp->pool, i));
+	}
+	kv_destroy(mp->pool);
+	free(mp);
+}
+/* --- END: memory pool --- */
+
+/* --- BEGIN: utilities --- */
+static khash_t(64) *bsw2_connectivity(const bwtl_t *b)
+{
+	khash_t(64) *h;
+	uint32_t k, l, cntk[4], cntl[4]; // this is fine
+	uint64_t x;
+	khiter_t iter;
+	int j, ret;
+	kvec_t(uint64_t) stack;
+
+	kv_init(stack);
+	h = kh_init(64);
+	kh_resize(64, h, b->seq_len * 4);
+	x = b->seq_len;
+	kv_push(uint64_t, stack, x);
+	while (kv_size(stack)) {
+		x = kv_pop(stack);
+		k = x>>32; l = (uint32_t)x;
+		bwtl_2occ4(b, k-1, l, cntk, cntl);
+		for (j = 0; j != 4; ++j) {
+			k = b->L2[j] + cntk[j] + 1;
+			l = b->L2[j] + cntl[j];
+			if (k > l) continue;
+			x = (uint64_t)k << 32 | l;
+			iter = kh_put(64, h, x, &ret);
+			if (ret) { // if not present
+				kh_value(h, iter) = 1;
+				kv_push(uint64_t, stack, x);
+			} else ++kh_value(h, iter);
+		}
+	}
+	kv_destroy(stack);
+	//fprintf(stderr, "[bsw2_connectivity] %u nodes in the DAG\n", kh_size(h));
+	return h;
+}
+// pick up top T matches at a node
+static void cut_tail(bsw2entry_t *u, int T, bsw2entry_t *aux)
+{
+	int i, *a, n, x;
+	if (u->n <= T) return;
+	if (aux->max < u->n) {
+		aux->max = u->n;
+		aux->array = (bsw2cell_t*)realloc(aux->array, aux->max * sizeof(bsw2cell_t));
+	}
+	a = (int*)aux->array;
+	for (i = n = 0; i != u->n; ++i)
+		if (u->array[i].ql && u->array[i].G > 0)
+			a[n++] = -u->array[i].G;
+	if (n <= T) return;
+	x = -ks_ksmall(int, n, a, T);
+	n = 0;
+	for (i = 0; i < u->n; ++i) {
+		bsw2cell_t *p = u->array + i;
+		if (p->G == x) ++n;
+		if (p->G < x || (p->G == x && n >= T)) {
+			p->qk = p->ql = 0; p->G = 0;
+			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -1;
+		}
+	}
+}
+// remove duplicated cells
+static inline void remove_duplicate(bsw2entry_t *u, khash_t(qintv) *hash)
+{
+	int i, ret, j;
+	khiter_t k;
+	qintv_t key;
+	kh_clear(qintv, hash);
+	for (i = 0; i != u->n; ++i) {
+		bsw2cell_t *p = u->array + i;
+		if (p->ql == 0) continue;
+		key.k = p->qk; key.l = p->ql;
+		k = kh_put(qintv, hash, key, &ret);
+		j = -1;
+		if (ret == 0) {
+			if ((uint32_t)kh_value(hash, k) >= p->G) j = i;
+			else {
+				j = kh_value(hash, k)>>32;
+				kh_value(hash, k) = (uint64_t)i<<32 | p->G;
+			}
+		} else kh_value(hash, k) = (uint64_t)i<<32 | p->G;
+		if (j >= 0) {
+			p = u->array + j;
+			p->qk = p->ql = 0; p->G = 0;
+			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
+		}
+	}
+}
+// merge two entries
+static void merge_entry(const bsw2opt_t * __restrict opt, bsw2entry_t *u, bsw2entry_t *v, bwtsw2_t *b)
+{
+	int i;
+	if (u->n + v->n >= u->max) {
+		u->max = u->n + v->n;
+		u->array = (bsw2cell_t*)realloc(u->array, u->max * sizeof(bsw2cell_t));
+	}
+	for (i = 0; i != v->n; ++i) {
+		bsw2cell_t *p = v->array + i;
+		if (p->ppos >= 0) p->ppos += u->n;
+		if (p->cpos[0] >= 0) p->cpos[0] += u->n;
+		if (p->cpos[1] >= 0) p->cpos[1] += u->n;
+		if (p->cpos[2] >= 0) p->cpos[2] += u->n;
+		if (p->cpos[3] >= 0) p->cpos[3] += u->n;
+	}
+	memcpy(u->array + u->n, v->array, v->n * sizeof(bsw2cell_t));
+	u->n += v->n;
+}
+
+static inline bsw2cell_t *push_array_p(bsw2entry_t *e)
+{
+	if (e->n == e->max) {
+		e->max = e->max? e->max<<1 : 256;
+		e->array = (bsw2cell_t*)realloc(e->array, sizeof(bsw2cell_t) * e->max);
+	}
+	return e->array + e->n;
+}
+
+static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
+{
+	long t1 = (curr->ru_utime.tv_sec - last->ru_utime.tv_sec) + (curr->ru_stime.tv_sec - last->ru_stime.tv_sec);
+	long t2 = (curr->ru_utime.tv_usec - last->ru_utime.tv_usec) + (curr->ru_stime.tv_usec - last->ru_stime.tv_usec);
+	return (double)t1 + t2 * 1e-6;
+}
+/* --- END: utilities --- */
+
+/* --- BEGIN: processing partial hits --- */
+static void save_hits(const bwtl_t *bwt, int thres, bsw2hit_t *hits, bsw2entry_t *u)
+{
+	int i;
+	uint32_t k; // this is fine
+	for (i = 0; i < u->n; ++i) {
+		bsw2cell_t *p = u->array + i;
+		if (p->G < thres) continue;
+		for (k = u->tk; k <= u->tl; ++k) {
+			int beg, end;
+			bsw2hit_t *q = 0;
+			beg = bwt->sa[k]; end = beg + p->tlen;
+			if (p->G > hits[beg*2].G) {
+				hits[beg*2+1] = hits[beg*2];
+				q = hits + beg * 2;
+			} else if (p->G > hits[beg*2+1].G) q = hits + beg * 2 + 1;
+			if (q) {
+				q->k = p->qk; q->l = p->ql; q->len = p->qlen; q->G = p->G;
+				q->beg = beg; q->end = end; q->G2 = q->k == q->l? 0 : q->G;
+				q->flag = q->n_seeds = 0;
+			}
+		}
+	}
+}
+/* "narrow hits" are node-to-node hits that have a high score and
+ * are not so repetitive (|SA interval|<=IS). */
+static void save_narrow_hits(const bwtl_t *bwtl, bsw2entry_t *u, bwtsw2_t *b1, int t, int IS)
+{
+	int i;
+	for (i = 0; i < u->n; ++i) {
+		bsw2hit_t *q;
+		bsw2cell_t *p = u->array + i;
+		if (p->G >= t && p->ql - p->qk + 1 <= IS) { // good narrow hit
+			if (b1->max == b1->n) {
+				b1->max = b1->max? b1->max<<1 : 4;
+				b1->hits = realloc(b1->hits, b1->max * sizeof(bsw2hit_t));
+			}
+			q = &b1->hits[b1->n++];
+			q->k = p->qk; q->l = p->ql;
+			q->len = p->qlen;
+			q->G = p->G; q->G2 = 0;
+			q->beg = bwtl->sa[u->tk]; q->end = q->beg + p->tlen;
+			q->flag = 0;
+			// delete p
+			p->qk = p->ql = 0; p->G = 0;
+			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
+		}
+	}
+}
+/* after this, "narrow SA hits" will be expanded and the coordinates
+ * will be obtained and stored in b->hits[*].k. */
+int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS)
+{
+	int i, j, n, is_rev;
+	if (b->n == 0) return 0;
+	if (bwt && bns) { // convert to chromosomal coordinates if requested
+		int old_n = b->n;
+		bsw2hit_t *old_hits = b->hits;
+		for (i = n = 0; i < b->n; ++i) { // compute the memory to allocated
+			bsw2hit_t *p = old_hits + i;
+			if (p->l - p->k + 1 <= IS) n += p->l - p->k + 1;
+			else if (p->G > 0) ++n;
+		}
+		b->n = b->max = n;
+		b->hits = calloc(b->max, sizeof(bsw2hit_t));
+		for (i = j = 0; i < old_n; ++i) {
+			bsw2hit_t *p = old_hits + i;
+			if (p->l - p->k + 1 <= IS) { // the hit is no so repetitive
+				bwtint_t k;
+				if (p->G == 0 && p->k == 0 && p->l == 0 && p->len == 0) continue;
+				for (k = p->k; k <= p->l; ++k) {
+					b->hits[j] = *p;
+					b->hits[j].k = bns_depos(bns, bwt_sa(bwt, k), &is_rev);
+					b->hits[j].l = 0;
+					b->hits[j].is_rev = is_rev;
+					if (is_rev) b->hits[j].k -= p->len - 1;
+					++j;
+				}
+			} else if (p->G > 0) {
+				b->hits[j] = *p;
+				b->hits[j].k = bns_depos(bns, bwt_sa(bwt, p->k), &is_rev);
+				b->hits[j].l = 0;
+				b->hits[j].flag |= 1;
+				b->hits[j].is_rev = is_rev;
+				if (is_rev) b->hits[j].k -= p->len - 1;
+				++j;
+			}
+		}
+		free(old_hits);
+	}
+	for (i = j = 0; i < b->n; ++i) // squeeze out empty elements
+		if (b->hits[i].G) b->hits[j++] = b->hits[i];
+	b->n = j;
+	ks_introsort(hitG, b->n, b->hits);
+	for (i = 1; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		for (j = 0; j < i; ++j) {
+			bsw2hit_t *q = b->hits + j;
+			int compatible = 1;
+			if (p->is_rev != q->is_rev) continue; // hits from opposite strands are not duplicates
+			if (p->l == 0 && q->l == 0) {
+				int qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg); // length of query overlap
+				if (qol < 0) qol = 0;
+				if ((float)qol / (p->end - p->beg) > MASK_LEVEL || (float)qol / (q->end - q->beg) > MASK_LEVEL) {
+					int64_t tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
+						- (int64_t)(p->k > q->k? p->k : q->k); // length of target overlap
+					if ((double)tol / p->len > MASK_LEVEL || (double)tol / q->len > MASK_LEVEL)
+						compatible = 0;
+				}
+			}
+			if (!compatible) {
+				p->G = 0;
+				if (q->G2 < p->G2) q->G2 = p->G2;
+				break;
+			}
+		}
+	}
+	n = i;
+	for (i = j = 0; i < n; ++i) {
+		if (b->hits[i].G == 0) continue;
+		if (i != j) b->hits[j++] = b->hits[i];
+		else ++j;
+	}
+	b->n = j;
+	return b->n;
+}
+
+int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
+{
+	int i, j, n;
+	if (b->n == 0) return 0;
+	ks_introsort(hitG, b->n, b->hits);
+	{ // choose a random one
+		int G0 = b->hits[0].G;
+		for (i = 1; i < b->n; ++i)
+			if (b->hits[i].G != G0) break;
+		j = (int)(i * drand48());
+		if (j) {
+			bsw2hit_t tmp;
+			tmp = b->hits[0]; b->hits[0] = b->hits[j]; b->hits[j] = tmp;
+		}
+	}
+	for (i = 1; i < b->n; ++i) {
+		bsw2hit_t *p = b->hits + i;
+		int all_compatible = 1;
+		if (p->G == 0) break;
+		for (j = 0; j < i; ++j) {
+			bsw2hit_t *q = b->hits + j;
+			int64_t tol = 0;
+			int qol, compatible = 0;
+			float fol;
+			if (q->G == 0) continue;
+			qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
+			if (qol < 0) qol = 0;
+			if (p->l == 0 && q->l == 0) {
+				tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
+					- (p->k > q->k? p->k : q->k);
+				if (tol < 0) tol = 0;
+			}
+			fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
+			if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
+			if (!compatible) {
+				if (q->G2 < p->G) q->G2 = p->G;
+				all_compatible = 0;
+			}
+		}
+		if (!all_compatible) p->G = 0;
+	}
+	n = i;
+	for (i = j = 0; i < n; ++i) {
+		if (b->hits[i].G == 0) continue;
+		if (i != j) b->hits[j++] = b->hits[i];
+		else ++j;
+	}
+	b->n = j;
+	return j;
+}
+/* --- END: processing partial hits --- */
+
+/* --- BEGIN: global mem pool --- */
+bsw2global_t *bsw2_global_init()
+{
+	bsw2global_t *pool;
+	bsw2stack_t *stack;
+	pool = calloc(1, sizeof(bsw2global_t));
+	stack = calloc(1, sizeof(bsw2stack_t));
+	stack->pool = (mempool_t*)calloc(1, sizeof(mempool_t));
+	pool->stack = (void*)stack;
+	return pool;
+}
+
+void bsw2_global_destroy(bsw2global_t *pool)
+{
+	stack_destroy((bsw2stack_t*)pool->stack);
+	free(pool->aln_mem);
+	free(pool);
+}
+/* --- END: global mem pool --- */
+
+static inline int fill_cell(const bsw2opt_t *o, int match_score, bsw2cell_t *c[4])
+{
+	int G = c[3]? c[3]->G + match_score : MINUS_INF;
+	if (c[1]) {
+		c[0]->I = c[1]->I > c[1]->G - o->q? c[1]->I - o->r : c[1]->G - o->qr;
+		if (c[0]->I > G) G = c[0]->I;
+	} else c[0]->I = MINUS_INF;
+	if (c[2]) {
+		c[0]->D = c[2]->D > c[2]->G - o->q? c[2]->D - o->r : c[2]->G - o->qr;
+		if (c[0]->D > G) G = c[0]->D;
+	} else c[0]->D = MINUS_INF;
+	return(c[0]->G = G);
+}
+
+static void init_bwtsw2(const bwtl_t *target, const bwt_t *query, bsw2stack_t *s)
+{
+	bsw2entry_t *u;
+	bsw2cell_t *x;
+
+	u = mp_alloc(s->pool);
+	u->tk = 0; u->tl = target->seq_len;
+	x = push_array_p(u);
+	*x = g_default_cell;
+	x->G = 0; x->qk = 0; x->ql = query->seq_len;
+	u->n++;
+	stack_push0(s, u);
+}
+/* On return, ret[1] keeps not-so-repetitive hits (narrow SA hits); ret[0] keeps all hits (right?) */
+bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool)
+{
+	bsw2stack_t *stack = (bsw2stack_t*)pool->stack;
+	bwtsw2_t *b, *b1, **b_ret;
+	int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
+	struct rusage curr, last;
+	khash_t(qintv) *rhash;
+	khash_t(64) *chash;
+
+	// initialize connectivity hash (chash)
+	chash = bsw2_connectivity(target);
+	// calculate score matrix
+	for (i = 0; i != 4; ++i)
+		for (j = 0; j != 4; ++j)
+			score_mat[i<<2|j] = (i == j)? opt->a : -opt->b;
+	// initialize other variables
+	rhash = kh_init(qintv);
+	init_bwtsw2(target, query, stack);
+	heap_size = opt->z;
+	heap = calloc(heap_size, sizeof(int));
+	// initialize the return struct
+	b = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
+	b->n = b->max = target->seq_len * 2;
+	b->hits = calloc(b->max, sizeof(bsw2hit_t));
+	b1 = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
+	b_ret = calloc(2, sizeof(void*));
+	b_ret[0] = b; b_ret[1] = b1;
+	// initialize timer
+	getrusage(0, &last);
+	// the main loop: traversal of the DAG
+	while (!stack_isempty(stack)) {
+		int old_n, tj;
+		bsw2entry_t *v;
+		uint32_t tcntk[4], tcntl[4];
+		bwtint_t k, l;
+
+		v = stack_pop(stack); old_n = v->n;
+		n_tot += v->n;
+
+		for (i = 0; i < v->n; ++i) { // test max depth and band width
+			bsw2cell_t *p = v->array + i;
+			if (p->ql == 0) continue;
+			if (p->tlen - (int)p->qlen > opt->bw || (int)p->qlen - p->tlen > opt->bw) {
+				p->qk = p->ql = 0;
+				if (p->ppos >= 0) v->array[p->ppos].cpos[p->pj] = -5;
+			}
+		}
+
+		// get Occ for the DAG
+		bwtl_2occ4(target, v->tk - 1, v->tl, tcntk, tcntl);
+		for (tj = 0; tj != 4; ++tj) { // descend to the children
+			bwtint_t qcntk[4], qcntl[4];
+			int qj, *curr_score_mat = score_mat + tj * 4;
+			khiter_t iter;
+			bsw2entry_t *u;
+
+			k = target->L2[tj] + tcntk[tj] + 1;
+			l = target->L2[tj] + tcntl[tj];
+			if (k > l) continue;
+			// update counter
+			iter = kh_get(64, chash, (uint64_t)k<<32 | l);
+			--kh_value(chash, iter);
+			// initialization
+			u = mp_alloc(stack->pool);
+			u->tk = k; u->tl = l;
+			memset(heap, 0, sizeof(int) * opt->z);
+			// loop through all the nodes in v
+		    for (i = 0; i < v->n; ++i) {
+				bsw2cell_t *p = v->array + i, *x, *c[4]; // c[0]=>current, c[1]=>I, c[2]=>D, c[3]=>G
+				int is_added = 0;
+				if (p->ql == 0) continue; // deleted node
+				c[0] = x = push_array_p(u);
+				x->G = MINUS_INF;
+				p->upos = x->upos = -1;
+				if (p->ppos >= 0) { // parent has been visited
+					c[1] = (v->array[p->ppos].upos >= 0)? u->array + v->array[p->ppos].upos : 0;
+					c[3] = v->array + p->ppos; c[2] = p;
+					if (fill_cell(opt, curr_score_mat[p->pj], c) > 0) { // then update topology at p and x
+						x->ppos = v->array[p->ppos].upos; // the parent pos in u
+						p->upos = u->n++; // the current pos in u
+						if (x->ppos >= 0) u->array[x->ppos].cpos[p->pj] = p->upos; // the child pos of its parent in u
+						is_added = 1;
+					}
+				} else {
+					x->D = p->D > p->G - opt->q? p->D - opt->r : p->G - opt->qr;
+					if (x->D > 0) {
+						x->G = x->D;
+						x->I = MINUS_INF; x->ppos = -1;
+						p->upos = u->n++;
+						is_added = 1;
+					}
+				}
+				if (is_added) { // x has been added to u->array. fill the remaining variables
+					x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
+					x->pj = p->pj; x->qk = p->qk; x->ql = p->ql; x->qlen = p->qlen; x->tlen = p->tlen + 1;
+					if (x->G > -heap[0]) {
+						heap[0] = -x->G;
+						ks_heapadjust(int, 0, heap_size, heap);
+					}
+				}
+				if ((x->G > opt->qr && x->G >= -heap[0]) || i < old_n) { // good node in u, or in v
+					if (p->cpos[0] == -1 || p->cpos[1] == -1 || p->cpos[2] == -1 || p->cpos[3] == -1) {
+						bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl);
+						for (qj = 0; qj != 4; ++qj) { // descend to the prefix trie
+							if (p->cpos[qj] != -1) continue; // this node will be visited later
+							k = query->L2[qj] + qcntk[qj] + 1;
+							l = query->L2[qj] + qcntl[qj];
+							if (k > l) { p->cpos[qj] = -2; continue; }
+							x = push_array_p(v);
+							p = v->array + i; // p may not point to the correct position after realloc
+							x->G = x->I = x->D = MINUS_INF;
+							x->qk = k; x->ql = l; x->pj = qj; x->qlen = p->qlen + 1; x->ppos = i; x->tlen = p->tlen;
+							x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
+							p->cpos[qj] = v->n++;
+						} // ~for(qj)
+					} // ~if(p->cpos[])
+				} // ~if
+			} // ~for(i)
+			if (u->n) save_hits(target, opt->t, b->hits, u);
+			{ // push u to the stack (or to the pending array)
+				uint32_t cnt, pos;
+				cnt = (uint32_t)kh_value(chash, iter);
+				pos = kh_value(chash, iter)>>32;
+				if (pos) { // something in the pending array, then merge
+					bsw2entry_t *w = kv_A(stack->pending, pos-1);
+					if (u->n) {
+						if (w->n < u->n) { // swap
+							w = u; u = kv_A(stack->pending, pos-1); kv_A(stack->pending, pos-1) = w;
+						}
+						merge_entry(opt, w, u, b);
+					}
+					if (cnt == 0) { // move from pending to stack0
+						remove_duplicate(w, rhash);
+						save_narrow_hits(target, w, b1, opt->t, opt->is);
+						cut_tail(w, opt->z, u);
+						stack_push0(stack, w);
+						kv_A(stack->pending, pos-1) = 0;
+						--stack->n_pending;
+					}
+					mp_free(stack->pool, u);
+				} else if (cnt) { // the first time
+					if (u->n) { // push to the pending queue
+						++stack->n_pending;
+						kv_push(bsw2entry_p, stack->pending, u);
+						kh_value(chash, iter) = (uint64_t)kv_size(stack->pending)<<32 | cnt;
+					} else mp_free(stack->pool, u);
+				} else { // cnt == 0, then push to the stack
+					bsw2entry_t *w = mp_alloc(stack->pool);
+					save_narrow_hits(target, u, b1, opt->t, opt->is);
+					cut_tail(u, opt->z, w);
+					mp_free(stack->pool, w);
+					stack_push0(stack, u);
+				}
+			}
+		} // ~for(tj)
+		mp_free(stack->pool, v);
+	} // while(top)
+	getrusage(0, &curr);
+	for (i = 0; i < 2; ++i)
+		for (j = 0; j < b_ret[i]->n; ++j)
+			b_ret[i]->hits[j].n_seeds = 0;
+	bsw2_resolve_duphits(bns, query, b, opt->is);
+	bsw2_resolve_duphits(bns, query, b1, opt->is);
+	//fprintf(stderr, "stats: %.3lf sec; %d elems\n", time_elapse(&curr, &last), n_tot);
+	// free
+	free(heap);
+	kh_destroy(qintv, rhash);
+	kh_destroy(64, chash);
+	stack->pending.n = stack->stack0.n = 0;
+	return b_ret;
+}

bwtsw2_main.c

@@ -0,0 +1,89 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
+#include "bwt.h"
+#include "bwtsw2.h"
+#include "utils.h"
+#include "bwa.h"
+
+int bwa_bwtsw2(int argc, char *argv[])
+{
+	bsw2opt_t *opt;
+	bwaidx_t *idx;
+	int c;
+
+	opt = bsw2_init_opt();
+	srand48(11);
+	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:MI:SG:C")) >= 0) {
+		switch (c) {
+		case 'q': opt->q = atoi(optarg); break;
+		case 'r': opt->r = atoi(optarg); break;
+		case 'a': opt->a = atoi(optarg); break;
+		case 'b': opt->b = atoi(optarg); break;
+		case 'w': opt->bw = atoi(optarg); break;
+		case 'T': opt->t = atoi(optarg); break;
+		case 't': opt->n_threads = atoi(optarg); break;
+		case 'z': opt->z = atoi(optarg); break;
+		case 's': opt->is = atoi(optarg); break;
+		case 'm': opt->mask_level = atof(optarg); break;
+		case 'c': opt->coef = atof(optarg); break;
+		case 'N': opt->t_seeds = atoi(optarg); break;
+		case 'M': opt->multi_2nd = 1; break;
+		case 'H': opt->hard_clip = 1; break;
+		case 'f': xreopen(optarg, "w", stdout); break;
+		case 'I': opt->max_ins = atoi(optarg); break;
+		case 'S': opt->skip_sw = 1; break;
+		case 'C': opt->cpy_cmt = 1; break;
+		case 'G': opt->max_chain_gap = atoi(optarg); break;
+		default: return 1;
+		}
+	}
+	opt->qr = opt->q + opt->r;
+
+	if (optind + 2 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa bwasw [options] <target.prefix> <query.fa> [query2.fa]\n\n");
+		fprintf(stderr, "Options: -a INT   score for a match [%d]\n", opt->a);
+		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
+		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
+		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
+		fprintf(stderr, "         -w INT   band width [%d]\n", opt->bw);
+		fprintf(stderr, "         -m FLOAT mask level [%.2f]\n", opt->mask_level);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n");
+		fprintf(stderr, "         -H       in SAM output, use hard clipping instead of soft clipping\n");
+		fprintf(stderr, "         -C       copy FASTA/Q comment to SAM output\n");
+		fprintf(stderr, "         -M       mark multi-part alignments as secondary\n");
+		fprintf(stderr, "         -S       skip Smith-Waterman read pairing\n");
+		fprintf(stderr, "         -I INT   ignore pairs with insert >=INT for inferring the size distr [%d]\n", opt->max_ins);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -T INT   score threshold divided by a [%d]\n", opt->t);
+		fprintf(stderr, "         -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
+		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
+		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
+		fprintf(stderr, "         -N INT   # seeds to trigger rev aln; 2*INT is also the chaining threshold [%d]\n", opt->t_seeds);
+		fprintf(stderr, "         -G INT   maximum gap size during chaining [%d]\n", opt->max_chain_gap);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
+		fprintf(stderr, "      BACs, the default setting usually works well. For the current PacBio\n");
+		fprintf(stderr, "      reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");
+		fprintf(stderr, "      increase '-z' for better sensitivity.\n");
+		fprintf(stderr, "\n");
+
+		return 1;
+	}
+
+	// adjust opt for opt->a
+	opt->t *= opt->a;
+	opt->coef *= opt->a;
+
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
+	bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
+	bwa_idx_destroy(idx);
+	free(opt);
+	
+	return 0;
+}

bwtsw2_pair.c

@@ -0,0 +1,274 @@
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "utils.h"
+#include "bwt.h"
+#include "bntseq.h"
+#include "bwtsw2.h"
+#include "kstring.h"
+#include "ksw.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define MIN_RATIO     0.8
+#define OUTLIER_BOUND 2.0
+#define MAX_STDDEV    4.0
+#define EXT_STDDEV    4.0
+
+typedef struct {
+	int low, high, failed;
+	double avg, std;
+} bsw2pestat_t;
+
+bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
+{
+	int i, k, x, p25, p50, p75, tmp, max_len = 0;
+	uint64_t *isize;
+	bsw2pestat_t r;
+
+	memset(&r, 0, sizeof(bsw2pestat_t));
+	isize = calloc(n, 8);
+	for (i = k = 0; i < n; i += 2) {
+		bsw2hit_t *t[2];
+		int l;
+		if (buf[i] == 0 || buf[i]->n != 1 || buf[i+1]->n != 1) continue; // more than 1 hits
+		t[0] = &buf[i]->hits[0]; t[1] = &buf[i+1]->hits[0];
+		if (t[0]->G2 > 0.8 * t[0]->G) continue; // the best hit is not good enough
+		if (t[1]->G2 > 0.8 * t[1]->G) continue; // the best hit is not good enough
+		l = t[0]->k > t[1]->k? t[0]->k - t[1]->k + t[1]->len : t[1]->k - t[0]->k + t[0]->len;
+		if (l >= max_ins) continue; // skip pairs with excessively large insert
+		max_len = max_len > t[0]->end - t[0]->beg? max_len : t[0]->end - t[0]->beg;
+		max_len = max_len > t[1]->end - t[1]->beg? max_len : t[1]->end - t[1]->beg;
+		isize[k++] = l;
+	}
+	ks_introsort_64(k, isize);
+	p25 = isize[(int)(.25 * k + .499)];
+	p50 = isize[(int)(.50 * k + .499)];
+	p75 = isize[(int)(.75 * k + .499)];
+	ksprintf(msg, "[%s] infer the insert size distribution from %d high-quality pairs.\n", __func__, k);
+	if (k < 8) {
+		ksprintf(msg, "[%s] fail to infer the insert size distribution: too few good pairs.\n", __func__);
+		free(isize);
+		r.failed = 1;
+		return r;
+	}
+	tmp    = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
+	r.low  = tmp > max_len? tmp : max_len;
+	if (r.low < 1) r.low = 1;
+	r.high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
+	if (r.low > r.high) {
+		ksprintf(msg, "[%s] fail to infer the insert size distribution: upper bound is smaller than max read length.\n", __func__);
+		free(isize);
+		r.failed = 1;
+		return r;
+	}
+	ksprintf(msg, "[%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
+	ksprintf(msg, "[%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r.low, r.high);
+	for (i = x = 0, r.avg = 0; i < k; ++i)
+		if (isize[i] >= r.low && isize[i] <= r.high)
+			r.avg += isize[i], ++x;
+	if (x == 0) {
+		ksprintf(msg, "[%s] fail to infer the insert size distribution: no pairs within boundaries.\n", __func__);
+		free(isize);
+		r.failed = 1;
+		return r;
+	}
+	r.avg /= x;
+	for (i = 0, r.std = 0; i < k; ++i)
+		if (isize[i] >= r.low && isize[i] <= r.high)
+			r.std += (isize[i] - r.avg) * (isize[i] - r.avg);
+	r.std = sqrt(r.std / x);
+	ksprintf(msg, "[%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r.avg, r.std);
+	tmp  = (int)(p25 - 3. * (p75 - p25) + .499);
+	r.low  = tmp > max_len? tmp : max_len;
+	if (r.low < 1) r.low = 1;
+	r.high = (int)(p75 + 3. * (p75 - p25) + .499);
+	if (r.low > r.avg - MAX_STDDEV * r.std) r.low = (int)(r.avg - MAX_STDDEV * r.std + .499);
+	r.low = tmp > max_len? tmp : max_len;
+	if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
+	ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
+	free(isize);
+	return r;
+}
+
+typedef struct {
+	int n_cigar, beg, end, len;
+	int64_t pos;
+	uint32_t *cigar;
+} pairaux_t;
+
+extern unsigned char nst_nt4_table[256];
+
+void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const bsw2pestat_t *st, const bsw2hit_t *h, int l_mseq, const char *mseq, bsw2hit_t *a, int8_t g_mat[25])
+{
+	extern void seq_reverse(int len, ubyte_t *seq, int is_comp);
+	int64_t k, beg, end;
+	uint8_t *seq, *ref;
+	int i;
+	// compute the region start and end
+	a->n_seeds = 1; a->flag |= BSW2_FLAG_MATESW; // before calling this routine, *a has been cleared with memset(0); the flag is set with 1<<6/7
+	if (h->is_rev == 0) {
+		beg = (int64_t)(h->k + st->avg - EXT_STDDEV * st->std - l_mseq + .499);
+		if (beg < h->k) beg = h->k;
+		end = (int64_t)(h->k + st->avg + EXT_STDDEV * st->std + .499);
+		a->is_rev = 1; a->flag |= 16;
+	} else {
+		beg = (int64_t)(h->k + h->end - h->beg - st->avg - EXT_STDDEV * st->std + .499);
+		end = (int64_t)(h->k + h->end - h->beg - st->avg + EXT_STDDEV * st->std + l_mseq + .499);
+		if (end > h->k + (h->end - h->beg)) end = h->k + (h->end - h->beg);
+		a->is_rev = 0;
+	}
+	if (beg < 1) beg = 1;
+	if (end > l_pac) end = l_pac;
+	if (end - beg < l_mseq) return;
+	// generate the sequence
+	seq = malloc(l_mseq + (end - beg));
+	ref = seq + l_mseq;
+	for (k = beg; k < end; ++k)
+		ref[k - beg] = pac[k>>2] >> ((~k&3)<<1) & 0x3;
+	if (h->is_rev == 0) {
+		for (i = 0; i < l_mseq; ++i) { // on the reverse strand
+			int c = nst_nt4_table[(int)mseq[i]];
+			seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
+		}
+	} else {
+		for (i = 0; i < l_mseq; ++i) // on the forward strand
+			seq[i] = nst_nt4_table[(int)mseq[i]];
+	}
+	{
+		int flag = KSW_XSUBO | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0) | opt->t;
+		kswr_t aln;
+		aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0);
+		a->G = aln.score;
+		a->G2 = aln.score2;
+		if (a->G < opt->t) a->G = 0;
+		if (a->G2 < opt->t) a->G2 = 0;
+		if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
+		a->k = beg + aln.tb;
+		a->len = aln.te - aln.tb + 1;
+		a->beg = aln.qb;
+		a->end = aln.qe + 1;
+		/*
+		printf("[Q] "); for (i = 0; i < l_mseq; ++i) putchar("ACGTN"[(int)seq[i]]); putchar('\n');
+		printf("[R] "); for (i = 0; i < end - beg; ++i) putchar("ACGTN"[(int)ref[i]]); putchar('\n');
+		printf("G=%d,G2=%d,beg=%d,end=%d,k=%lld,len=%d\n", a->G, a->G2, a->beg, a->end, a->k, a->len);
+		*/
+	}
+	if (a->is_rev) i = a->beg, a->beg = l_mseq - a->end, a->end = l_mseq - i;
+	free(seq);
+}
+
+void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hits)
+{
+	extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
+	bsw2pestat_t pes;
+	int i, j, k, n_rescued = 0, n_moved = 0, n_fixed = 0;
+	int8_t g_mat[25];
+	kstring_t msg;
+	memset(&msg, 0, sizeof(kstring_t));
+	pes = bsw2_stat(n, hits, &msg, opt->max_ins);
+	for (i = k = 0; i < 5; ++i) {
+		for (j = 0; j < 4; ++j)
+			g_mat[k++] = i == j? opt->a : -opt->b;
+		g_mat[k++] = 0;
+	}
+	for (i = 0; i < n; i += 2) {
+		bsw2hit_t a[2];
+		memset(&a, 0, sizeof(bsw2hit_t) * 2);
+		a[0].flag = 1<<6; a[1].flag = 1<<7;
+		for (j = 0; j < 2; ++j) { // set the read1/2 flag
+			if (hits[i+j] == 0) continue;
+			for (k = 0; k < hits[i+j]->n; ++k) {
+				bsw2hit_t *p = &hits[i+j]->hits[k];
+				p->flag |= 1<<(6+j);
+			}
+		}
+		if (pes.failed) continue;
+		if (hits[i] == 0 || hits[i+1] == 0) continue; // one end has excessive N
+		if (hits[i]->n != 1 && hits[i+1]->n != 1) continue; // no end has exactly one hit
+		if (hits[i]->n > 1 || hits[i+1]->n > 1) continue; // one read has more than one hit
+		if (!opt->skip_sw) {
+			if (hits[i+0]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+0]->hits[0], seq[i+1].l, seq[i+1].seq, &a[1], g_mat);
+			if (hits[i+1]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+1]->hits[0], seq[i+0].l, seq[i+0].seq, &a[0], g_mat);
+		} // else a[0].G == a[1].G == a[0].G2 == a[1].G2 == 0
+		// the following enumerate all possibilities. It is tedious but necessary...
+		if (hits[i]->n + hits[i+1]->n == 1) { // one end mapped; the other not;
+			bwtsw2_t *p[2];
+			int which;
+			if (hits[i]->n == 1) p[0] = hits[i], p[1] = hits[i+1], which = 1;
+			else p[0] = hits[i+1], p[1] = hits[i], which = 0;
+			if (a[which].G == 0) continue;
+			a[which].flag |= BSW2_FLAG_RESCUED;
+			if (p[1]->max == 0) {
+				p[1]->max = 1;
+				p[1]->hits = malloc(sizeof(bsw2hit_t));
+			}
+			p[1]->hits[0] = a[which];
+			p[1]->n = 1;
+			p[0]->hits[0].flag |= 2;
+			p[1]->hits[0].flag |= 2;
+			++n_rescued;
+		} else { // then both ends mapped
+			int is_fixed = 0;
+			//fprintf(stderr, "%d; %lld,%lld; %d,%d\n", a[0].is_rev, hits[i]->hits[0].k, a[0].k, hits[i]->hits[0].end, a[0].end);
+			for (j = 0; j < 2; ++j) { // fix wrong mappings and wrong suboptimal alignment score
+				bsw2hit_t *p = &hits[i+j]->hits[0];
+				if (p->G < a[j].G) { // the orginal mapping is suboptimal
+					a[j].G2 = a[j].G2 > p->G? a[j].G2 : p->G; // FIXME: reset BSW2_FLAG_TANDEM?
+					*p = a[j];
+					++n_fixed;
+					is_fixed = 1;
+				} else if (p->k != a[j].k && p->G2 < a[j].G) {
+					p->G2 = a[j].G;
+				} else if (p->k == a[j].k && p->G2 < a[j].G2) {
+					p->G2 = a[j].G2;
+				}
+			}
+			if (hits[i]->hits[0].k == a[0].k && hits[i+1]->hits[0].k == a[1].k) { // properly paired and no ends need to be moved
+				for (j = 0; j < 2; ++j)
+					hits[i+j]->hits[0].flag |= 2 | (a[j].flag & BSW2_FLAG_TANDEM);
+			} else if (hits[i]->hits[0].k == a[0].k || hits[i+1]->hits[0].k == a[1].k) { // a tandem match
+				for (j = 0; j < 2; ++j) {
+					hits[i+j]->hits[0].flag |= 2;
+					if (hits[i+j]->hits[0].k != a[j].k)
+						hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM;
+				}
+			} else if (!is_fixed && (a[0].G || a[1].G)) { // it is possible to move one end
+				if (a[0].G && a[1].G) { // now we have two "proper pairs"
+					int G[2];
+					double diff;
+					G[0] = hits[i]->hits[0].G + a[1].G;
+					G[1] = hits[i+1]->hits[0].G + a[0].G;
+					diff = fabs((double)(G[0] - G[1])) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.);
+					if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0;
+				}
+				if (a[0].G == 0 || a[1].G == 0) { // one proper pair only
+					bsw2hit_t *p[2]; // p[0] points the unchanged hit; p[1] to the hit to be moved
+					int which, isize;
+					double dev, diff;
+					if (a[0].G) p[0] = &hits[i+1]->hits[0], p[1] = &hits[i]->hits[0], which = 0;
+					else p[0] = &hits[i]->hits[0], p[1] = &hits[i+1]->hits[0], which = 1;
+					isize = p[0]->is_rev? p[0]->k + p[0]->len - a[which].k : a[which].k + a[which].len - p[0]->k;
+					dev = fabs(isize - pes.avg) / pes.std;
+					diff = (double)(p[1]->G - a[which].G) / (opt->a + opt->b) / (p[1]->end - p[1]->beg) * 100.0;
+					if (diff < dev * 2.) { // then move (heuristic)
+						a[which].G2 = a[which].G;
+						p[1][0] = a[which];
+						p[1]->flag |= BSW2_FLAG_MOVED | 2;
+						p[0]->flag |= 2;
+						++n_moved;
+					}
+				}
+			} else if (is_fixed) {
+				hits[i+0]->hits[0].flag |= 2;
+				hits[i+1]->hits[0].flag |= 2;
+			}
+		}
+	}
+	ksprintf(&msg, "[%s] #fixed=%d, #rescued=%d, #moved=%d\n", __func__, n_fixed, n_rescued, n_moved);
+	fputs(msg.s, stderr);
+	free(msg.s);
+}

code_of_conduct.md

@@ -0,0 +1,30 @@
+## Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all
+people who contribute through reporting issues, posting feature requests,
+updating documentation, submitting pull requests or patches, and other
+activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual
+language or imagery, derogatory comments or personal attacks, trolling, public
+or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct. Project maintainers or
+contributors who do not follow the Code of Conduct may be removed from the
+project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by opening an issue or contacting the maintainer via email.
+
+This Code of Conduct is adapted from the [Contributor Covenant][cc], [version
+1.0.0][v1].
+
+[cc]: http://contributor-covenant.org/
+[v1]: http://contributor-covenant.org/version/1/0/0/

example.c

@@ -0,0 +1,60 @@
+#include <stdio.h>
+#include <zlib.h>
+#include <string.h>
+#include <errno.h>
+#include <assert.h>
+#include "bwamem.h"
+#include "kseq.h" // for the FASTA/Q parser
+KSEQ_DECLARE(gzFile)
+
+int main(int argc, char *argv[])
+{
+	bwaidx_t *idx;
+	gzFile fp;
+	kseq_t *ks;
+	mem_opt_t *opt;
+
+	if (argc < 3) {
+		fprintf(stderr, "Usage: bwamem-lite <idx.base> <reads.fq>\n");
+		return 1;
+	}
+
+	idx = bwa_idx_load(argv[1], BWA_IDX_ALL); // load the BWA index
+	if (NULL == idx) {
+		fprintf(stderr, "Index load failed.\n");
+		exit(EXIT_FAILURE);
+	}
+	fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
+	if (NULL == fp) {
+		fprintf(stderr, "Couldn't open %s : %s\n",
+				strcmp(argv[2], "-") ? argv[2] : "stdin",
+				errno ? strerror(errno) : "Out of memory");
+		exit(EXIT_FAILURE);
+	}
+	ks = kseq_init(fp); // initialize the FASTA/Q parser
+	opt = mem_opt_init(); // initialize the BWA-MEM parameters to the default values
+
+	while (kseq_read(ks) >= 0) { // read one sequence
+		mem_alnreg_v ar;
+		int i, k;
+		ar = mem_align1(opt, idx->bwt, idx->bns, idx->pac, ks->seq.l, ks->seq.s); // get all the hits
+		for (i = 0; i < ar.n; ++i) { // traverse each hit
+			mem_aln_t a;
+			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
+			a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
+			// print alignment
+			printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
+			for (k = 0; k < a.n_cigar; ++k) // print CIGAR
+				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
+			printf("\t%d\n", a.NM); // print edit distance
+			free(a.cigar); // don't forget to deallocate CIGAR
+		}
+		free(ar.a); // and deallocate the hit list
+	}
+
+	free(opt);
+	kseq_destroy(ks);
+	gzclose(fp);
+	bwa_idx_destroy(idx);
+	return 0;
+}

fastmap.c

@@ -0,0 +1,483 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <zlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+#include <ctype.h>
+#include <math.h>
+#include "bwa.h"
+#include "bwamem.h"
+#include "kvec.h"
+#include "utils.h"
+#include "bntseq.h"
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+extern unsigned char nst_nt4_table[256];
+
+void *kopen(const char *fn, int *_fd);
+int kclose(void *a);
+void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_data, int n_steps);
+
+typedef struct {
+	kseq_t *ks, *ks2;
+	mem_opt_t *opt;
+	mem_pestat_t *pes0;
+	int64_t n_processed;
+	int copy_comment, actual_chunk_size;
+	bwaidx_t *idx;
+} ktp_aux_t;
+
+typedef struct {
+	ktp_aux_t *aux;
+	int n_seqs;
+	bseq1_t *seqs;
+} ktp_data_t;
+
+static void *process(void *shared, int step, void *_data)
+{
+	ktp_aux_t *aux = (ktp_aux_t*)shared;
+	ktp_data_t *data = (ktp_data_t*)_data;
+	int i;
+	if (step == 0) {
+		ktp_data_t *ret;
+		int64_t size = 0;
+		ret = calloc(1, sizeof(ktp_data_t));
+		ret->seqs = bseq_read(aux->actual_chunk_size, &ret->n_seqs, aux->ks, aux->ks2);
+		if (ret->seqs == 0) {
+			free(ret);
+			return 0;
+		}
+		if (!aux->copy_comment)
+			for (i = 0; i < ret->n_seqs; ++i) {
+				free(ret->seqs[i].comment);
+				ret->seqs[i].comment = 0;
+			}
+		for (i = 0; i < ret->n_seqs; ++i) size += ret->seqs[i].l_seq;
+		if (bwa_verbose >= 3)
+			fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, ret->n_seqs, (long)size);
+		return ret;
+	} else if (step == 1) {
+		const mem_opt_t *opt = aux->opt;
+		const bwaidx_t *idx = aux->idx;
+		if (opt->flag & MEM_F_SMARTPE) {
+			bseq1_t *sep[2];
+			int n_sep[2];
+			mem_opt_t tmp_opt = *opt;
+			bseq_classify(data->n_seqs, data->seqs, n_sep, sep);
+			if (bwa_verbose >= 3)
+				fprintf(stderr, "[M::%s] %d single-end sequences; %d paired-end sequences\n", __func__, n_sep[0], n_sep[1]);
+			if (n_sep[0]) {
+				tmp_opt.flag &= ~MEM_F_PE;
+				mem_process_seqs(&tmp_opt, idx->bwt, idx->bns, idx->pac, aux->n_processed, n_sep[0], sep[0], 0);
+				for (i = 0; i < n_sep[0]; ++i)
+					data->seqs[sep[0][i].id].sam = sep[0][i].sam;
+			}
+			if (n_sep[1]) {
+				tmp_opt.flag |= MEM_F_PE;
+				mem_process_seqs(&tmp_opt, idx->bwt, idx->bns, idx->pac, aux->n_processed + n_sep[0], n_sep[1], sep[1], aux->pes0);
+				for (i = 0; i < n_sep[1]; ++i)
+					data->seqs[sep[1][i].id].sam = sep[1][i].sam;
+			}
+			free(sep[0]); free(sep[1]);
+		} else mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, aux->n_processed, data->n_seqs, data->seqs, aux->pes0);
+		aux->n_processed += data->n_seqs;
+		return data;
+	} else if (step == 2) {
+		for (i = 0; i < data->n_seqs; ++i) {
+			if (data->seqs[i].sam) err_fputs(data->seqs[i].sam, stdout);
+			free(data->seqs[i].name); free(data->seqs[i].comment);
+			free(data->seqs[i].seq); free(data->seqs[i].qual); free(data->seqs[i].sam);
+		}
+		free(data->seqs); free(data);
+		return 0;
+	}
+	return 0;
+}
+
+static void update_a(mem_opt_t *opt, const mem_opt_t *opt0)
+{
+	if (opt0->a) { // matching score is changed
+		if (!opt0->b) opt->b *= opt->a;
+		if (!opt0->T) opt->T *= opt->a;
+		if (!opt0->o_del) opt->o_del *= opt->a;
+		if (!opt0->e_del) opt->e_del *= opt->a;
+		if (!opt0->o_ins) opt->o_ins *= opt->a;
+		if (!opt0->e_ins) opt->e_ins *= opt->a;
+		if (!opt0->zdrop) opt->zdrop *= opt->a;
+		if (!opt0->pen_clip5) opt->pen_clip5 *= opt->a;
+		if (!opt0->pen_clip3) opt->pen_clip3 *= opt->a;
+		if (!opt0->pen_unpaired) opt->pen_unpaired *= opt->a;
+	}
+}
+
+int main_mem(int argc, char *argv[])
+{
+	mem_opt_t *opt, opt0;
+	int fd, fd2, i, c, ignore_alt = 0, no_mt_io = 0;
+	int fixed_chunk_size = -1;
+	gzFile fp, fp2 = 0;
+	char *p, *rg_line = 0, *hdr_line = 0;
+	const char *mode = 0;
+	void *ko = 0, *ko2 = 0;
+	mem_pestat_t pes[4];
+	ktp_aux_t aux;
+
+	memset(&aux, 0, sizeof(ktp_aux_t));
+	memset(pes, 0, 4 * sizeof(mem_pestat_t));
+	for (i = 0; i < 4; ++i) pes[i].failed = 1;
+
+	aux.opt = opt = mem_opt_init();
+	memset(&opt0, 0, sizeof(mem_opt_t));
+	while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:F:z:")) >= 0) {
+		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
+		else if (c == '1') no_mt_io = 1;
+		else if (c == 'x') mode = optarg;
+		else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
+		else if (c == 'A') opt->a = atoi(optarg), opt0.a = 1;
+		else if (c == 'B') opt->b = atoi(optarg), opt0.b = 1;
+		else if (c == 'T') opt->T = atoi(optarg), opt0.T = 1;
+		else if (c == 'U') opt->pen_unpaired = atoi(optarg), opt0.pen_unpaired = 1;
+		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
+		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
+		else if (c == 'a') opt->flag |= MEM_F_ALL;
+		else if (c == 'p') opt->flag |= MEM_F_PE | MEM_F_SMARTPE;
+		else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
+		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
+		else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
+		else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
+		else if (c == '5') opt->flag |= MEM_F_PRIMARY5 | MEM_F_KEEP_SUPP_MAPQ; // always apply MEM_F_KEEP_SUPP_MAPQ with -5
+		else if (c == 'q') opt->flag |= MEM_F_KEEP_SUPP_MAPQ;
+		else if (c == 'u') opt->flag |= MEM_F_XB;
+		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
+		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
+		else if (c == 'v') bwa_verbose = atoi(optarg);
+		else if (c == 'j') ignore_alt = 1;
+		else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.;
+		else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.;
+		else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1;
+		else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
+		else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
+		else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
+		else if (c == 'o' || c == 'f') xreopen(optarg, "wb", stdout);
+		else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
+		else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
+		else if (c == 'C') aux.copy_comment = 1;
+		else if (c == 'K') fixed_chunk_size = atoi(optarg);
+		else if (c == 'X') opt->mask_level = atof(optarg);
+		else if (c == 'F') bwa_dbg = atoi(optarg);
+		else if (c == 'h') {
+			opt0.max_XA_hits = opt0.max_XA_hits_alt = 1;
+			opt->max_XA_hits = opt->max_XA_hits_alt = strtol(optarg, &p, 10);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				opt->max_XA_hits_alt = strtol(p+1, &p, 10);
+		}
+		else if (c == 'z') opt->XA_drop_ratio = atof(optarg);
+		else if (c == 'Q') {
+			opt0.mapQ_coef_len = 1;
+			opt->mapQ_coef_len = atoi(optarg);
+			opt->mapQ_coef_fac = opt->mapQ_coef_len > 0? log(opt->mapQ_coef_len) : 0;
+		} else if (c == 'O') {
+			opt0.o_del = opt0.o_ins = 1;
+			opt->o_del = opt->o_ins = strtol(optarg, &p, 10);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				opt->o_ins = strtol(p+1, &p, 10);
+		} else if (c == 'E') {
+			opt0.e_del = opt0.e_ins = 1;
+			opt->e_del = opt->e_ins = strtol(optarg, &p, 10);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				opt->e_ins = strtol(p+1, &p, 10);
+		} else if (c == 'L') {
+			opt0.pen_clip5 = opt0.pen_clip3 = 1;
+			opt->pen_clip5 = opt->pen_clip3 = strtol(optarg, &p, 10);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				opt->pen_clip3 = strtol(p+1, &p, 10);
+		} else if (c == 'R') {
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
+		} else if (c == 'H') {
+			if (optarg[0] != '@') {
+				FILE *fp;
+				if ((fp = fopen(optarg, "r")) != 0) {
+					char *buf;
+					buf = calloc(1, 0x10000);
+					while (fgets(buf, 0xffff, fp)) {
+						i = strlen(buf);
+						assert(buf[i-1] == '\n'); // a long line
+						buf[i-1] = 0;
+						hdr_line = bwa_insert_header(buf, hdr_line);
+					}
+					free(buf);
+					fclose(fp);
+				}
+			} else hdr_line = bwa_insert_header(optarg, hdr_line);
+		} else if (c == 'I') { // specify the insert size distribution
+			aux.pes0 = pes;
+			pes[1].failed = 0;
+			pes[1].avg = strtod(optarg, &p);
+			pes[1].std = pes[1].avg * .1;
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				pes[1].std = strtod(p+1, &p);
+			pes[1].high = (int)(pes[1].avg + 4. * pes[1].std + .499);
+			pes[1].low  = (int)(pes[1].avg - 4. * pes[1].std + .499);
+			if (pes[1].low < 1) pes[1].low = 1;
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				pes[1].high = (int)(strtod(p+1, &p) + .499);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				pes[1].low  = (int)(strtod(p+1, &p) + .499);
+			if (bwa_verbose >= 3)
+				fprintf(stderr, "[M::%s] mean insert size: %.3f, stddev: %.3f, max: %d, min: %d\n",
+						__func__, pes[1].avg, pes[1].std, pes[1].high, pes[1].low);
+		}
+		else return 1;
+	}
+
+	if (rg_line) {
+		hdr_line = bwa_insert_header(rg_line, hdr_line);
+		free(rg_line);
+	}
+
+	if (opt->n_threads < 1) opt->n_threads = 1;
+	if (optind + 1 >= argc || optind + 3 < argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
+		fprintf(stderr, "Algorithm options:\n\n");
+		fprintf(stderr, "       -t INT        number of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "       -k INT        minimum seed length [%d]\n", opt->min_seed_len);
+		fprintf(stderr, "       -w INT        band width for banded alignment [%d]\n", opt->w);
+		fprintf(stderr, "       -d INT        off-diagonal X-dropoff [%d]\n", opt->zdrop);
+		fprintf(stderr, "       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
+		fprintf(stderr, "       -y INT        seed occurrence for the 3rd round seeding [%ld]\n", (long)opt->max_mem_intv);
+//		fprintf(stderr, "       -s INT        look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
+		fprintf(stderr, "       -c INT        skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
+		fprintf(stderr, "       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->drop_ratio);
+		fprintf(stderr, "       -W INT        discard a chain if seeded bases shorter than INT [0]\n");
+		fprintf(stderr, "       -m INT        perform at most INT rounds of mate rescues for each read [%d]\n", opt->max_matesw);
+		fprintf(stderr, "       -S            skip mate rescue\n");
+		fprintf(stderr, "       -P            skip pairing; mate rescue performed unless -S also in use\n");
+		fprintf(stderr, "\nScoring options:\n\n");
+		fprintf(stderr, "       -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [%d]\n", opt->a);
+		fprintf(stderr, "       -B INT        penalty for a mismatch [%d]\n", opt->b);
+		fprintf(stderr, "       -O INT[,INT]  gap open penalties for deletions and insertions [%d,%d]\n", opt->o_del, opt->o_ins);
+		fprintf(stderr, "       -E INT[,INT]  gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins);
+		fprintf(stderr, "       -L INT[,INT]  penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
+		fprintf(stderr, "       -U INT        penalty for an unpaired read pair [%d]\n\n", opt->pen_unpaired);
+		fprintf(stderr, "       -x STR        read type. Setting -x changes multiple parameters unless overridden [null]\n");
+		fprintf(stderr, "                     pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  (PacBio reads to ref)\n");
+		fprintf(stderr, "                     ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0  (Oxford Nanopore 2D-reads to ref)\n");
+		fprintf(stderr, "                     intractg: -B9 -O16 -L5  (intra-species contigs to ref)\n");
+		fprintf(stderr, "\nInput/output options:\n\n");
+		fprintf(stderr, "       -p            smart pairing (ignoring in2.fq)\n");
+		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
+		fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
+		fprintf(stderr, "       -o FILE       sam file to output results to [stdout]\n");
+		fprintf(stderr, "       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
+		fprintf(stderr, "       -5            for split alignment, take the alignment with the smallest query (not genomic) coordinate as primary\n");
+		fprintf(stderr, "       -q            don't modify mapQ of supplementary alignments\n");
+		fprintf(stderr, "       -K INT        process INT input bases in each batch regardless of nThreads (for reproducibility) []\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "       -v INT        verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
+		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);
+		fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >%.2f%% of the max score, output all in XA [%d,%d]\n", 
+				opt->XA_drop_ratio * 100.0,
+				opt->max_XA_hits, opt->max_XA_hits_alt);
+		fprintf(stderr, "                     A second value may be given for alternate sequences.\n");
+		fprintf(stderr, "       -z FLOAT      The fraction of the max score to use with -h [%f].\n", opt->XA_drop_ratio);
+		fprintf(stderr, "                     specify the mean, standard deviation (10%% of the mean if absent), max\n");
+		fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");
+		fprintf(stderr, "       -C            append FASTA/FASTQ comment to SAM output\n");
+		fprintf(stderr, "       -V            output the reference FASTA header in the XR tag\n");
+		fprintf(stderr, "       -Y            use soft clipping for supplementary alignments\n");
+		fprintf(stderr, "       -M            mark shorter split hits as secondary\n\n");
+		fprintf(stderr, "       -I FLOAT[,FLOAT[,INT[,INT]]]\n");
+		fprintf(stderr, "                     specify the mean, standard deviation (10%% of the mean if absent), max\n");
+		fprintf(stderr, "                     (4 sigma from the mean if absent) and min of the insert size distribution.\n");
+		fprintf(stderr, "                     FR orientation only. [inferred]\n");
+		fprintf(stderr, "       -u            output XB instead of XA; XB is XA with the alignment score and mapping quality added.\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Note: Please read the man page for detailed description of the command line and options.\n");
+		fprintf(stderr, "\n");
+		free(opt);
+		return 1;
+	}
+
+	if (mode) {
+		if (strcmp(mode, "intractg") == 0) {
+			if (!opt0.o_del) opt->o_del = 16;
+			if (!opt0.o_ins) opt->o_ins = 16;
+			if (!opt0.b) opt->b = 9;
+			if (!opt0.pen_clip5) opt->pen_clip5 = 5;
+			if (!opt0.pen_clip3) opt->pen_clip3 = 5;
+		} else if (strcmp(mode, "pacbio") == 0 || strcmp(mode, "pbref") == 0 || strcmp(mode, "ont2d") == 0) {
+			if (!opt0.o_del) opt->o_del = 1;
+			if (!opt0.e_del) opt->e_del = 1;
+			if (!opt0.o_ins) opt->o_ins = 1;
+			if (!opt0.e_ins) opt->e_ins = 1;
+			if (!opt0.b) opt->b = 1;
+			if (opt0.split_factor == 0.) opt->split_factor = 10.;
+			if (strcmp(mode, "ont2d") == 0) {
+				if (!opt0.min_chain_weight) opt->min_chain_weight = 20;
+				if (!opt0.min_seed_len) opt->min_seed_len = 14;
+				if (!opt0.pen_clip5) opt->pen_clip5 = 0;
+				if (!opt0.pen_clip3) opt->pen_clip3 = 0;
+			} else {
+				if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
+				if (!opt0.min_seed_len) opt->min_seed_len = 17;
+				if (!opt0.pen_clip5) opt->pen_clip5 = 0;
+				if (!opt0.pen_clip3) opt->pen_clip3 = 0;
+			}
+		} else {
+			fprintf(stderr, "[E::%s] unknown read type '%s'\n", __func__, mode);
+			return 1; // FIXME memory leak
+		}
+	} else update_a(opt, &opt0);
+	bwa_fill_scmat(opt->a, opt->b, opt->mat);
+
+	aux.idx = bwa_idx_load_from_shm(argv[optind]);
+	if (aux.idx == 0) {
+		if ((aux.idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
+	} else if (bwa_verbose >= 3)
+		fprintf(stderr, "[M::%s] load the bwa index from shared memory\n", __func__);
+	if (ignore_alt)
+		for (i = 0; i < aux.idx->bns->n_seqs; ++i)
+			aux.idx->bns->anns[i].is_alt = 0;
+
+	ko = kopen(argv[optind + 1], &fd);
+	if (ko == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 1]);
+		return 1;
+	}
+	fp = gzdopen(fd, "r");
+	aux.ks = kseq_init(fp);
+	if (optind + 2 < argc) {
+		if (opt->flag&MEM_F_PE) {
+			if (bwa_verbose >= 2)
+				fprintf(stderr, "[W::%s] when '-p' is in use, the second query file is ignored.\n", __func__);
+		} else {
+			ko2 = kopen(argv[optind + 2], &fd2);
+			if (ko2 == 0) {
+				if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 2]);
+				return 1;
+			}
+			fp2 = gzdopen(fd2, "r");
+			aux.ks2 = kseq_init(fp2);
+			opt->flag |= MEM_F_PE;
+		}
+	}
+	bwa_print_sam_hdr(aux.idx->bns, hdr_line);
+	aux.actual_chunk_size = fixed_chunk_size > 0? fixed_chunk_size : opt->chunk_size * opt->n_threads;
+	kt_pipeline(no_mt_io? 1 : 2, process, &aux, 3);
+	free(hdr_line);
+	free(opt);
+	bwa_idx_destroy(aux.idx);
+	kseq_destroy(aux.ks);
+	err_gzclose(fp); kclose(ko);
+	if (aux.ks2) {
+		kseq_destroy(aux.ks2);
+		err_gzclose(fp2); kclose(ko2);
+	}
+	return 0;
+}
+
+int main_fastmap(int argc, char *argv[])
+{
+	int c, i, min_iwidth = 20, min_len = 17, print_seq = 0, min_intv = 1, max_len = INT_MAX;
+	uint64_t max_intv = 0;
+	kseq_t *seq;
+	bwtint_t k;
+	gzFile fp;
+	smem_i *itr;
+	const bwtintv_v *a;
+	bwaidx_t *idx;
+
+	while ((c = getopt(argc, argv, "w:l:pi:I:L:")) >= 0) {
+		switch (c) {
+			case 'p': print_seq = 1; break;
+			case 'w': min_iwidth = atoi(optarg); break;
+			case 'l': min_len = atoi(optarg); break;
+			case 'i': min_intv = atoi(optarg); break;
+			case 'I': max_intv = atol(optarg); break;
+			case 'L': max_len  = atoi(optarg); break;
+		    default: return 1;
+		}
+	}
+	if (optind + 1 >= argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa fastmap [options] <idxbase> <in.fq>\n\n");
+		fprintf(stderr, "Options: -l INT    min SMEM length to output [%d]\n", min_len);
+		fprintf(stderr, "         -w INT    max interval size to find coordiantes [%d]\n", min_iwidth);
+		fprintf(stderr, "         -i INT    min SMEM interval size [%d]\n", min_intv);
+		fprintf(stderr, "         -L INT    max MEM length [%d]\n", max_len);
+		fprintf(stderr, "         -I INT    stop if MEM is longer than -l with a size less than INT [%ld]\n", (long)max_intv);
+		fprintf(stderr, "\n");
+		return 1;
+	}
+
+	fp = xzopen(argv[optind + 1], "r");
+	seq = kseq_init(fp);
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
+	itr = smem_itr_init(idx->bwt);
+	smem_config(itr, min_intv, max_len, max_intv);
+	while (kseq_read(seq) >= 0) {
+		err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
+		if (print_seq) {
+			err_putchar('\t');
+			err_puts(seq->seq.s);
+		} else err_putchar('\n');
+		for (i = 0; i < seq->seq.l; ++i)
+			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
+		smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s);
+		while ((a = smem_next(itr)) != 0) {
+			for (i = 0; i < a->n; ++i) {
+				bwtintv_t *p = &a->a[i];
+				if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
+				err_printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
+				if (p->x[2] <= min_iwidth) {
+					for (k = 0; k < p->x[2]; ++k) {
+						bwtint_t pos;
+						int len, is_rev, ref_id;
+						len  = (uint32_t)p->info - (p->info>>32);
+						pos = bns_depos(idx->bns, bwt_sa(idx->bwt, p->x[0] + k), &is_rev);
+						if (is_rev) pos -= len - 1;
+						bns_cnt_ambi(idx->bns, pos, len, &ref_id);
+						err_printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
+					}
+				} else err_puts("\t*");
+				err_putchar('\n');
+			}
+		}
+		err_puts("//");
+	}
+
+	smem_itr_destroy(itr);
+	bwa_idx_destroy(idx);
+	kseq_destroy(seq);
+	err_gzclose(fp);
+	return 0;
+}

is.c

@@ -0,0 +1,223 @@
+/*
+ * sais.c for sais-lite
+ * Copyright (c) 2008 Yuta Mori All Rights Reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#include <stdlib.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef unsigned char ubyte_t;
+#define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
+
+/* find the start or end of each bucket */
+static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
+{
+	int i;
+	for (i = 0; i < k; ++i) C[i] = 0;
+	for (i = 0; i < n; ++i) ++C[chr(i)];
+}
+static void getBuckets(const int *C, int *B, int k, int end)
+{
+	int i, sum = 0;
+	if (end) {
+		for (i = 0; i < k; ++i) {
+			sum += C[i];
+			B[i] = sum;
+		}
+	} else {
+		for (i = 0; i < k; ++i) {
+			sum += C[i];
+			B[i] = sum - C[i];
+		}
+	}
+}
+
+/* compute SA */
+static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
+{
+	int *b, i, j;
+	int  c0, c1;
+	/* compute SAl */
+	if (C == B) getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 0);	/* find starts of buckets */
+	j = n - 1;
+	b = SA + B[c1 = chr(j)];
+	*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
+	for (i = 0; i < n; ++i) {
+		j = SA[i], SA[i] = ~j;
+		if (0 < j) {
+			--j;
+			if ((c0 = chr(j)) != c1) {
+				B[c1] = b - SA;
+				b = SA + B[c1 = c0];
+			}
+			*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
+		}
+	}
+	/* compute SAs */
+	if (C == B) getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
+		if (0 < (j = SA[i])) {
+			--j;
+			if ((c0 = chr(j)) != c1) {
+				B[c1] = b - SA;
+				b = SA + B[c1 = c0];
+			}
+			*--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
+		} else SA[i] = ~j;
+	}
+}
+
+/*
+ * find the suffix array SA of T[0..n-1] in {0..k-1}^n use a working
+ * space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
+ */
+static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
+{
+	int *C, *B, *RA;
+	int  i, j, c, m, p, q, plen, qlen, name;
+	int  c0, c1;
+	int  diff;
+
+	/* stage 1: reduce the problem by at least 1/2 sort all the
+	 * S-substrings */
+	if (k <= fs) {
+		C = SA + n;
+		B = (k <= (fs - k)) ? C + k : C;
+	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
+	getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = 0; i < n; ++i) SA[i] = 0;
+	for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+		if ((c0 = chr(i)) < (c1 + c)) c = 1;
+		else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
+	}
+	induceSA(T, SA, C, B, n, k, cs);
+	if (fs < k) free(C);
+	/* compact all the sorted substrings into the first m items of SA
+	 * 2*m must be not larger than n (proveable) */
+	for (i = 0, m = 0; i < n; ++i) {
+		p = SA[i];
+		if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
+			for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
+			if ((j < n) && (c0 < c1)) SA[m++] = p;
+		}
+	}
+	for (i = m; i < n; ++i) SA[i] = 0;	/* init the name array buffer */
+	/* store the length of all substrings */
+	for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+		if ((c0 = chr(i)) < (c1 + c)) c = 1;
+		else if (c != 0) {
+			SA[m + ((i + 1) >> 1)] = j - i - 1;
+			j = i + 1;
+			c = 0;
+		}
+	}
+	/* find the lexicographic names of all substrings */
+	for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
+		p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
+		if (plen == qlen) {
+			for (j = 0; (j < plen) && (chr(p + j) == chr(q + j)); j++);
+			if (j == plen) diff = 0;
+		}
+		if (diff != 0) ++name, q = p, qlen = plen;
+		SA[m + (p >> 1)] = name;
+	}
+
+	/* stage 2: solve the reduced problem recurse if names are not yet
+	 * unique */
+	if (name < m) {
+		RA = SA + n + fs - m;
+		for (i = n - 1, j = m - 1; m <= i; --i) {
+			if (SA[i] != 0) RA[j--] = SA[i] - 1;
+		}
+		if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
+		for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+			if ((c0 = chr(i)) < (c1 + c)) c = 1;
+			else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
+		}
+		for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
+	}
+	/* stage 3: induce the result for the original problem */
+	if (k <= fs) {
+		C = SA + n;
+		B = (k <= (fs - k)) ? C + k : C;
+	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
+	/* put all left-most S characters into their buckets */
+	getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
+	for (i = m - 1; 0 <= i; --i) {
+		j = SA[i], SA[i] = 0;
+		SA[--B[chr(j)]] = j;
+	}
+	induceSA(T, SA, C, B, n, k, cs);
+	if (fs < k) free(C);
+	return 0;
+}
+
+/**
+ * Constructs the suffix array of a given string.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n] The output array of suffixes.
+ * @param n The length of the given string.
+ * @return 0 if no error occurred
+ */
+int is_sa(const ubyte_t *T, int *SA, int n)
+{
+	if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
+	SA[0] = n;
+	if (n <= 1) {
+		if (n == 1) SA[1] = 0;
+		return 0;
+	}
+	return sais_main(T, SA+1, 0, n, 256, 1);
+}
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string.
+ * @param T[0..n-1] The input string.
+ * @param n The length of the given string.
+ * @return The primary index if no error occurred, -1 or -2 otherwise.
+ */
+int is_bwt(ubyte_t *T, int n)
+{
+	int *SA, i, primary = 0;
+	SA = (int*)calloc(n+1, sizeof(int));
+
+	if (is_sa(T, SA, n)) return -1;
+
+	for (i = 0; i <= n; ++i) {
+		if (SA[i] == 0) primary = i;
+		else SA[i] = T[SA[i] - 1];
+	}
+	for (i = 0; i < primary; ++i) T[i] = SA[i];
+	for (; i < n; ++i) T[i] = SA[i + 1];
+	free(SA);
+	return primary;
+}

kbtree.h

@@ -0,0 +1,388 @@
+/*-
+ * Copyright 1997-1999, 2001, John-Mark Gurney.
+ *           2008-2009, Attractive Chaos <attractor@live.co.uk>
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+#ifndef __AC_KBTREE_H
+#define __AC_KBTREE_H
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdint.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef struct {
+	int32_t is_internal:1, n:31;
+} kbnode_t;
+
+#define	__KB_KEY(type, x)	((type*)((char*)x + 4))
+#define __KB_PTR(btr, x)	((kbnode_t**)((char*)x + btr->off_ptr))
+
+#define __KB_TREE_T(name)						\
+	typedef struct {							\
+		kbnode_t *root;							\
+		int	off_key, off_ptr, ilen, elen;		\
+		int	n, t;								\
+		int	n_keys, n_nodes;					\
+	} kbtree_##name##_t;
+
+#define __KB_INIT(name, key_t)											\
+	kbtree_##name##_t *kb_init_##name(int size)							\
+	{																	\
+		kbtree_##name##_t *b;											\
+		b = (kbtree_##name##_t*)calloc(1, sizeof(kbtree_##name##_t));	\
+		b->t = ((size - 4 - sizeof(void*)) / (sizeof(void*) + sizeof(key_t)) + 1) >> 1; \
+		if (b->t < 2) {													\
+			free(b); return 0;											\
+		}																\
+		b->n = 2 * b->t - 1;											\
+		b->off_ptr = 4 + b->n * sizeof(key_t);							\
+		b->ilen = (4 + sizeof(void*) + b->n * (sizeof(void*) + sizeof(key_t)) + 3) >> 2 << 2; \
+		b->elen = (b->off_ptr + 3) >> 2 << 2;							\
+		b->root = (kbnode_t*)calloc(1, b->ilen);						\
+		++b->n_nodes;													\
+		return b;														\
+	}
+
+#define __kb_destroy(b) do {											\
+		int i, max = 8;													\
+		kbnode_t *x, **top, **stack = 0;								\
+		if (b) {														\
+			top = stack = (kbnode_t**)calloc(max, sizeof(kbnode_t*));	\
+			*top++ = (b)->root;											\
+			while (top != stack) {										\
+				x = *--top;												\
+				if (x == 0 || x->is_internal == 0) { free(x); continue; } \
+				for (i = 0; i <= x->n; ++i)								\
+					if (__KB_PTR(b, x)[i]) {							\
+						if (top - stack == max) {						\
+							max <<= 1;									\
+							stack = (kbnode_t**)realloc(stack, max * sizeof(kbnode_t*)); \
+							top = stack + (max>>1);						\
+						}												\
+						*top++ = __KB_PTR(b, x)[i];						\
+					}													\
+				free(x);												\
+			}															\
+		}																\
+		free(b); free(stack);											\
+	} while (0)
+
+#define __kb_get_first(key_t, b, ret) do {	\
+		kbnode_t *__x = (b)->root;			\
+		while (__KB_PTR(b, __x)[0] != 0)	\
+			__x = __KB_PTR(b, __x)[0];		\
+		(ret) = __KB_KEY(key_t, __x)[0];	\
+	} while (0)
+
+#define __KB_GET_AUX0(name, key_t, __cmp)								\
+	static inline int __kb_get_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
+	{																	\
+		int tr, *rr, begin, end, n = x->n >> 1;							\
+		if (x->n == 0) return -1;										\
+		if (__cmp(*k, __KB_KEY(key_t, x)[n]) < 0) {						\
+			begin = 0; end = n;											\
+		} else { begin = n; end = x->n - 1; }							\
+		rr = r? r : &tr;												\
+		n = end;														\
+		while (n >= begin && (*rr = __cmp(*k, __KB_KEY(key_t, x)[n])) < 0) --n; \
+		return n;														\
+	}
+
+#define __KB_GET_AUX1(name, key_t, __cmp)								\
+	static inline int __kb_getp_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
+	{																	\
+		int tr, *rr, begin = 0, end = x->n;								\
+		if (x->n == 0) return -1;										\
+		rr = r? r : &tr;												\
+		while (begin < end) {											\
+			int mid = (begin + end) >> 1;								\
+			if (__cmp(__KB_KEY(key_t, x)[mid], *k) < 0) begin = mid + 1; \
+			else end = mid;												\
+		}																\
+		if (begin == x->n) { *rr = 1; return x->n - 1; }				\
+		if ((*rr = __cmp(*k, __KB_KEY(key_t, x)[begin])) < 0) --begin;	\
+		return begin;													\
+	}
+
+#define __KB_GET(name, key_t)											\
+	static key_t *kb_getp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
+	{																	\
+		int i, r = 0;													\
+		kbnode_t *x = b->root;											\
+		while (x) {														\
+			i = __kb_getp_aux_##name(x, k, &r);							\
+			if (i >= 0 && r == 0) return &__KB_KEY(key_t, x)[i];		\
+			if (x->is_internal == 0) return 0;							\
+			x = __KB_PTR(b, x)[i + 1];									\
+		}																\
+		return 0;														\
+	}																	\
+	static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \
+	{																	\
+		return kb_getp_##name(b, &k);									\
+	}
+
+#define __KB_INTERVAL(name, key_t)										\
+	static void kb_intervalp_##name(kbtree_##name##_t *b, const key_t * __restrict k, key_t **lower, key_t **upper)	\
+	{																	\
+		int i, r = 0;													\
+		kbnode_t *x = b->root;											\
+		*lower = *upper = 0;											\
+		while (x) {														\
+			i = __kb_getp_aux_##name(x, k, &r);							\
+			if (i >= 0 && r == 0) {										\
+				*lower = *upper = &__KB_KEY(key_t, x)[i];				\
+				return;													\
+			}															\
+			if (i >= 0) *lower = &__KB_KEY(key_t, x)[i];				\
+			if (i < x->n - 1) *upper = &__KB_KEY(key_t, x)[i + 1];		\
+			if (x->is_internal == 0) return;							\
+			x = __KB_PTR(b, x)[i + 1];									\
+		}																\
+	}																	\
+	static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \
+	{																	\
+		kb_intervalp_##name(b, &k, lower, upper);						\
+	}
+
+#define __KB_PUT(name, key_t, __cmp)									\
+	/* x must be an internal node */									\
+	static void __kb_split_##name(kbtree_##name##_t *b, kbnode_t *x, int i, kbnode_t *y) \
+	{																	\
+		kbnode_t *z;													\
+		z = (kbnode_t*)calloc(1, y->is_internal? b->ilen : b->elen);	\
+		++b->n_nodes;													\
+		z->is_internal = y->is_internal;								\
+		z->n = b->t - 1;												\
+		memcpy(__KB_KEY(key_t, z), __KB_KEY(key_t, y) + b->t, sizeof(key_t) * (b->t - 1)); \
+		if (y->is_internal) memcpy(__KB_PTR(b, z), __KB_PTR(b, y) + b->t, sizeof(void*) * b->t); \
+		y->n = b->t - 1;												\
+		memmove(__KB_PTR(b, x) + i + 2, __KB_PTR(b, x) + i + 1, sizeof(void*) * (x->n - i)); \
+		__KB_PTR(b, x)[i + 1] = z;										\
+		memmove(__KB_KEY(key_t, x) + i + 1, __KB_KEY(key_t, x) + i, sizeof(key_t) * (x->n - i)); \
+		__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[b->t - 1];			\
+		++x->n;															\
+	}																	\
+	static void __kb_putp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k) \
+	{																	\
+		int i = x->n - 1;												\
+		if (x->is_internal == 0) {										\
+			i = __kb_getp_aux_##name(x, k, 0);							\
+			if (i != x->n - 1)											\
+				memmove(__KB_KEY(key_t, x) + i + 2, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
+			__KB_KEY(key_t, x)[i + 1] = *k;								\
+			++x->n;														\
+		} else {														\
+			i = __kb_getp_aux_##name(x, k, 0) + 1;						\
+			if (__KB_PTR(b, x)[i]->n == 2 * b->t - 1) {					\
+				__kb_split_##name(b, x, i, __KB_PTR(b, x)[i]);			\
+				if (__cmp(*k, __KB_KEY(key_t, x)[i]) > 0) ++i;			\
+			}															\
+			__kb_putp_aux_##name(b, __KB_PTR(b, x)[i], k);				\
+		}																\
+	}																	\
+	static void kb_putp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
+	{																	\
+		kbnode_t *r, *s;												\
+		++b->n_keys;													\
+		r = b->root;													\
+		if (r->n == 2 * b->t - 1) {										\
+			++b->n_nodes;												\
+			s = (kbnode_t*)calloc(1, b->ilen);							\
+			b->root = s; s->is_internal = 1; s->n = 0;					\
+			__KB_PTR(b, s)[0] = r;										\
+			__kb_split_##name(b, s, 0, r);								\
+			r = s;														\
+		}																\
+		__kb_putp_aux_##name(b, r, k);									\
+	}																	\
+	static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \
+	{																	\
+		kb_putp_##name(b, &k);											\
+	}
+
+
+#define __KB_DEL(name, key_t)											\
+	static key_t __kb_delp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k, int s) \
+	{																	\
+		int yn, zn, i, r = 0;											\
+		kbnode_t *xp, *y, *z;											\
+		key_t kp;														\
+		if (x == 0) return *k;											\
+		if (s) { /* s can only be 0, 1 or 2 */							\
+			r = x->is_internal == 0? 0 : s == 1? 1 : -1;				\
+			i = s == 1? x->n - 1 : -1;									\
+		} else i = __kb_getp_aux_##name(x, k, &r);						\
+		if (x->is_internal == 0) {										\
+			if (s == 2) ++i;											\
+			kp = __KB_KEY(key_t, x)[i];									\
+			memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
+			--x->n;														\
+			return kp;													\
+		}																\
+		if (r == 0) {													\
+			if ((yn = __KB_PTR(b, x)[i]->n) >= b->t) {					\
+				xp = __KB_PTR(b, x)[i];									\
+				kp = __KB_KEY(key_t, x)[i];								\
+				__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 1); \
+				return kp;												\
+			} else if ((zn = __KB_PTR(b, x)[i + 1]->n) >= b->t) {		\
+				xp = __KB_PTR(b, x)[i + 1];								\
+				kp = __KB_KEY(key_t, x)[i];								\
+				__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 2); \
+				return kp;												\
+			} else if (yn == b->t - 1 && zn == b->t - 1) {				\
+				y = __KB_PTR(b, x)[i]; z = __KB_PTR(b, x)[i + 1];		\
+				__KB_KEY(key_t, y)[y->n++] = *k;						\
+				memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, z), z->n * sizeof(key_t)); \
+				if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, z), (z->n + 1) * sizeof(void*)); \
+				y->n += z->n;											\
+				memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
+				memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
+				--x->n;													\
+				free(z);												\
+				return __kb_delp_aux_##name(b, y, k, s);				\
+			}															\
+		}																\
+		++i;															\
+		if ((xp = __KB_PTR(b, x)[i])->n == b->t - 1) {					\
+			if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n >= b->t) {		\
+				memmove(__KB_KEY(key_t, xp) + 1, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
+				if (xp->is_internal) memmove(__KB_PTR(b, xp) + 1, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
+				__KB_KEY(key_t, xp)[0] = __KB_KEY(key_t, x)[i - 1];		\
+				__KB_KEY(key_t, x)[i - 1] = __KB_KEY(key_t, y)[y->n - 1]; \
+				if (xp->is_internal) __KB_PTR(b, xp)[0] = __KB_PTR(b, y)[y->n]; \
+				--y->n; ++xp->n;										\
+			} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n >= b->t) { \
+				__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i];	\
+				__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[0];			\
+				if (xp->is_internal) __KB_PTR(b, xp)[xp->n] = __KB_PTR(b, y)[0]; \
+				--y->n;													\
+				memmove(__KB_KEY(key_t, y), __KB_KEY(key_t, y) + 1, y->n * sizeof(key_t)); \
+				if (y->is_internal) memmove(__KB_PTR(b, y), __KB_PTR(b, y) + 1, (y->n + 1) * sizeof(void*)); \
+			} else if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n == b->t - 1) { \
+				__KB_KEY(key_t, y)[y->n++] = __KB_KEY(key_t, x)[i - 1];	\
+				memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, xp), xp->n * sizeof(key_t));	\
+				if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
+				y->n += xp->n;											\
+				memmove(__KB_KEY(key_t, x) + i - 1, __KB_KEY(key_t, x) + i, (x->n - i) * sizeof(key_t)); \
+				memmove(__KB_PTR(b, x) + i, __KB_PTR(b, x) + i + 1, (x->n - i) * sizeof(void*)); \
+				--x->n;													\
+				free(xp);												\
+				xp = y;													\
+			} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n == b->t - 1) { \
+				__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i];	\
+				memmove(__KB_KEY(key_t, xp) + xp->n, __KB_KEY(key_t, y), y->n * sizeof(key_t));	\
+				if (xp->is_internal) memmove(__KB_PTR(b, xp) + xp->n, __KB_PTR(b, y), (y->n + 1) * sizeof(void*)); \
+				xp->n += y->n;											\
+				memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
+				memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
+				--x->n;													\
+				free(y);												\
+			}															\
+		}																\
+		return __kb_delp_aux_##name(b, xp, k, s);						\
+	}																	\
+	static key_t kb_delp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
+	{																	\
+		kbnode_t *x;													\
+		key_t ret;														\
+		ret = __kb_delp_aux_##name(b, b->root, k, 0);					\
+		--b->n_keys;													\
+		if (b->root->n == 0 && b->root->is_internal) {					\
+			--b->n_nodes;												\
+			x = b->root;												\
+			b->root = __KB_PTR(b, x)[0];								\
+			free(x);													\
+		}																\
+		return ret;														\
+	}																	\
+	static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \
+	{																	\
+		return kb_delp_##name(b, &k);									\
+	}
+
+typedef struct {
+	kbnode_t *x;
+	int i;
+} __kbstack_t;
+
+#define __kb_traverse(key_t, b, __func) do {							\
+		int __kmax = 8;													\
+		__kbstack_t *__kstack, *__kp;									\
+		__kp = __kstack = (__kbstack_t*)calloc(__kmax, sizeof(__kbstack_t)); \
+		__kp->x = (b)->root; __kp->i = 0;								\
+		for (;;) {														\
+			while (__kp->x && __kp->i <= __kp->x->n) {					\
+				if (__kp - __kstack == __kmax - 1) {					\
+					__kmax <<= 1;										\
+					__kstack = (__kbstack_t*)realloc(__kstack, __kmax * sizeof(__kbstack_t)); \
+					__kp = __kstack + (__kmax>>1) - 1;					\
+				}														\
+				(__kp+1)->i = 0; (__kp+1)->x = __kp->x->is_internal? __KB_PTR(b, __kp->x)[__kp->i] : 0; \
+				++__kp;													\
+			}															\
+			--__kp;														\
+			if (__kp >= __kstack) {										\
+				if (__kp->x && __kp->i < __kp->x->n) __func(&__KB_KEY(key_t, __kp->x)[__kp->i]); \
+				++__kp->i;												\
+			} else break;												\
+		}																\
+		free(__kstack);													\
+	} while (0)
+
+#define KBTREE_INIT(name, key_t, __cmp)			\
+	__KB_TREE_T(name)							\
+	__KB_INIT(name, key_t)						\
+	__KB_GET_AUX1(name, key_t, __cmp)			\
+	__KB_GET(name, key_t)						\
+	__KB_INTERVAL(name, key_t)					\
+	__KB_PUT(name, key_t, __cmp)				\
+	__KB_DEL(name, key_t)
+
+#define KB_DEFAULT_SIZE 512
+
+#define kbtree_t(name) kbtree_##name##_t
+#define kb_init(name, s) kb_init_##name(s)
+#define kb_destroy(name, b) __kb_destroy(b)
+#define kb_get(name, b, k) kb_get_##name(b, k)
+#define kb_put(name, b, k) kb_put_##name(b, k)
+#define kb_del(name, b, k) kb_del_##name(b, k)
+#define kb_interval(name, b, k, l, u) kb_interval_##name(b, k, l, u)
+#define kb_getp(name, b, k) kb_getp_##name(b, k)
+#define kb_putp(name, b, k) kb_putp_##name(b, k)
+#define kb_delp(name, b, k) kb_delp_##name(b, k)
+#define kb_intervalp(name, b, k, l, u) kb_intervalp_##name(b, k, l, u)
+
+#define kb_size(b) ((b)->n_keys)
+
+#define kb_generic_cmp(a, b) (((b) < (a)) - ((a) < (b)))
+#define kb_str_cmp(a, b) strcmp(a, b)
+
+#endif

khash.h

@@ -0,0 +1,614 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  An example:
+
+#include "khash.h"
+KHASH_MAP_INIT_INT(32, char)
+int main() {
+	int ret, is_missing;
+	khiter_t k;
+	khash_t(32) *h = kh_init(32);
+	k = kh_put(32, h, 5, &ret);
+	kh_value(h, k) = 10;
+	k = kh_get(32, h, 10);
+	is_missing = (k == kh_end(h));
+	k = kh_get(32, h, 5);
+	kh_del(32, h, k);
+	for (k = kh_begin(h); k != kh_end(h); ++k)
+		if (kh_exist(h, k)) kh_value(h, k) = 1;
+	kh_destroy(32, h);
+	return 0;
+}
+*/
+
+/*
+  2011-12-29 (0.2.7):
+
+    * Minor code clean up; no actual effect.
+
+  2011-09-16 (0.2.6):
+
+	* The capacity is a power of 2. This seems to dramatically improve the
+	  speed for simple keys. Thank Zilong Tan for the suggestion. Reference:
+
+	   - http://code.google.com/p/ulib/
+	   - http://nothings.org/computer/judy/
+
+	* Allow to optionally use linear probing which usually has better
+	  performance for random input. Double hashing is still the default as it
+	  is more robust to certain non-random input.
+
+	* Added Wang's integer hash function (not used by default). This hash
+	  function is more robust to certain non-random input.
+
+  2011-02-14 (0.2.5):
+
+    * Allow to declare global functions.
+
+  2009-09-26 (0.2.4):
+
+    * Improve portability
+
+  2008-09-19 (0.2.3):
+
+	* Corrected the example
+	* Improved interfaces
+
+  2008-09-11 (0.2.2):
+
+	* Improved speed a little in kh_put()
+
+  2008-09-10 (0.2.1):
+
+	* Added kh_clear()
+	* Fixed a compiling error
+
+  2008-09-02 (0.2.0):
+
+	* Changed to token concatenation which increases flexibility.
+
+  2008-08-31 (0.1.2):
+
+	* Fixed a bug in kh_get(), which has not been tested previously.
+
+  2008-08-31 (0.1.1):
+
+	* Added destructor
+*/
+
+
+#ifndef __AC_KHASH_H
+#define __AC_KHASH_H
+
+/*!
+  @header
+
+  Generic hash table library.
+ */
+
+#define AC_VERSION_KHASH_H "0.2.6"
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+/* compipler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifdef _MSC_VER
+#define kh_inline __inline
+#else
+#define kh_inline inline
+#endif
+
+typedef khint32_t khint_t;
+typedef khint_t khiter_t;
+
+#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
+#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
+#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
+#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
+#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
+#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
+#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
+
+#ifdef KHASH_LINEAR
+#define __ac_inc(k, m) 1
+#else
+#define __ac_inc(k, m) (((k)>>3 ^ (k)<<3) | 1) & (m)
+#endif
+
+#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4)
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef kcalloc
+#define kcalloc(N,Z) calloc(N,Z)
+#endif
+#ifndef kmalloc
+#define kmalloc(Z) malloc(Z)
+#endif
+#ifndef krealloc
+#define krealloc(P,Z) realloc(P,Z)
+#endif
+#ifndef kfree
+#define kfree(P) free(P)
+#endif
+
+static const double __ac_HASH_UPPER = 0.77;
+
+#define __KHASH_TYPE(name, khkey_t, khval_t) \
+	typedef struct { \
+		khint_t n_buckets, size, n_occupied, upper_bound; \
+		khint32_t *flags; \
+		khkey_t *keys; \
+		khval_t *vals; \
+	} kh_##name##_t;
+
+#define __KHASH_PROTOTYPES(name, khkey_t, khval_t)	 					\
+	extern kh_##name##_t *kh_init_##name(void);							\
+	extern void kh_destroy_##name(kh_##name##_t *h);					\
+	extern void kh_clear_##name(kh_##name##_t *h);						\
+	extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); 	\
+	extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
+	extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
+	extern void kh_del_##name(kh_##name##_t *h, khint_t x);
+
+#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	SCOPE kh_##name##_t *kh_init_##name(void) {							\
+		return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t));		\
+	}																	\
+	SCOPE void kh_destroy_##name(kh_##name##_t *h)						\
+	{																	\
+		if (h) {														\
+			kfree((void *)h->keys); kfree(h->flags);					\
+			kfree((void *)h->vals);										\
+			kfree(h);													\
+		}																\
+	}																	\
+	SCOPE void kh_clear_##name(kh_##name##_t *h)						\
+	{																	\
+		if (h && h->flags) {											\
+			memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \
+			h->size = h->n_occupied = 0;								\
+		}																\
+	}																	\
+	SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) 	\
+	{																	\
+		if (h->n_buckets) {												\
+			khint_t inc, k, i, last, mask;								\
+			mask = h->n_buckets - 1;									\
+			k = __hash_func(key); i = k & mask;							\
+			inc = __ac_inc(k, mask); last = i; /* inc==1 for linear probing */ \
+			while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+				i = (i + inc) & mask; 									\
+				if (i == last) return h->n_buckets;						\
+			}															\
+			return __ac_iseither(h->flags, i)? h->n_buckets : i;		\
+		} else return 0;												\
+	}																	\
+	SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+	{ /* This function uses 0.25*n_bucktes bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \
+		khint32_t *new_flags = 0;										\
+		khint_t j = 1;													\
+		{																\
+			kroundup32(new_n_buckets); 									\
+			if (new_n_buckets < 4) new_n_buckets = 4;					\
+			if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0;	/* requested size is too small */ \
+			else { /* hash table size to be changed (shrink or expand); rehash */ \
+				new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t));	\
+				if (!new_flags) return -1;								\
+				memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \
+				if (h->n_buckets < new_n_buckets) {	/* expand */		\
+					khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
+					if (!new_keys) return -1;							\
+					h->keys = new_keys;									\
+					if (kh_is_map) {									\
+						khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
+						if (!new_vals) return -1;						\
+						h->vals = new_vals;								\
+					}													\
+				} /* otherwise shrink */								\
+			}															\
+		}																\
+		if (j) { /* rehashing is needed */								\
+			for (j = 0; j != h->n_buckets; ++j) {						\
+				if (__ac_iseither(h->flags, j) == 0) {					\
+					khkey_t key = h->keys[j];							\
+					khval_t val;										\
+					khint_t new_mask;									\
+					new_mask = new_n_buckets - 1; 						\
+					if (kh_is_map) val = h->vals[j];					\
+					__ac_set_isdel_true(h->flags, j);					\
+					while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \
+						khint_t inc, k, i;								\
+						k = __hash_func(key);							\
+						i = k & new_mask;								\
+						inc = __ac_inc(k, new_mask);					\
+						while (!__ac_isempty(new_flags, i)) i = (i + inc) & new_mask; \
+						__ac_set_isempty_false(new_flags, i);			\
+						if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \
+							{ khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
+							if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
+							__ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \
+						} else { /* write the element and jump out of the loop */ \
+							h->keys[i] = key;							\
+							if (kh_is_map) h->vals[i] = val;			\
+							break;										\
+						}												\
+					}													\
+				}														\
+			}															\
+			if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \
+				h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
+				if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
+			}															\
+			kfree(h->flags); /* free the working space */				\
+			h->flags = new_flags;										\
+			h->n_buckets = new_n_buckets;								\
+			h->n_occupied = h->size;									\
+			h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
+		}																\
+		return 0;														\
+	}																	\
+	SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+	{																	\
+		khint_t x;														\
+		if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \
+			if (h->n_buckets > (h->size<<1)) {							\
+				if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \
+					*ret = -1; return h->n_buckets;						\
+				}														\
+			} else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \
+				*ret = -1; return h->n_buckets;							\
+			}															\
+		} /* TODO: to implement automatically shrinking; resize() already support shrinking */ \
+		{																\
+			khint_t inc, k, i, site, last, mask = h->n_buckets - 1;		\
+			x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \
+			if (__ac_isempty(h->flags, i)) x = i; /* for speed up */	\
+			else {														\
+				inc = __ac_inc(k, mask); last = i;						\
+				while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+					if (__ac_isdel(h->flags, i)) site = i;				\
+					i = (i + inc) & mask; 								\
+					if (i == last) { x = site; break; }					\
+				}														\
+				if (x == h->n_buckets) {								\
+					if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
+					else x = i;											\
+				}														\
+			}															\
+		}																\
+		if (__ac_isempty(h->flags, x)) { /* not present at all */		\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size; ++h->n_occupied;									\
+			*ret = 1;													\
+		} else if (__ac_isdel(h->flags, x)) { /* deleted */				\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size;													\
+			*ret = 2;													\
+		} else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \
+		return x;														\
+	}																	\
+	SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)				\
+	{																	\
+		if (x != h->n_buckets && !__ac_iseither(h->flags, x)) {			\
+			__ac_set_isdel_true(h->flags, x);							\
+			--h->size;													\
+		}																\
+	}
+
+#define KHASH_DECLARE(name, khkey_t, khval_t)		 					\
+	__KHASH_TYPE(name, khkey_t, khval_t) 								\
+	__KHASH_PROTOTYPES(name, khkey_t, khval_t)
+
+#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	__KHASH_TYPE(name, khkey_t, khval_t) 								\
+	__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+/* --- BEGIN OF HASH FUNCTIONS --- */
+
+/*! @function
+  @abstract     Integer hash function
+  @param  key   The integer [khint32_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int_hash_func(key) (khint32_t)(key)
+/*! @function
+  @abstract     Integer comparison function
+ */
+#define kh_int_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     64-bit integer hash function
+  @param  key   The integer [khint64_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
+/*! @function
+  @abstract     64-bit integer comparison function
+ */
+#define kh_int64_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     const char* hash function
+  @param  s     Pointer to a null terminated string
+  @return       The hash value
+ */
+static kh_inline khint_t __ac_X31_hash_string(const char *s)
+{
+	khint_t h = (khint_t)*s;
+	if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s;
+	return h;
+}
+/*! @function
+  @abstract     Another interface to const char* hash function
+  @param  key   Pointer to a null terminated string [const char*]
+  @return       The hash value [khint_t]
+ */
+#define kh_str_hash_func(key) __ac_X31_hash_string(key)
+/*! @function
+  @abstract     Const char* comparison function
+ */
+#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
+
+static kh_inline khint_t __ac_Wang_hash(khint_t key)
+{
+    key += ~(key << 15);
+    key ^=  (key >> 10);
+    key +=  (key << 3);
+    key ^=  (key >> 6);
+    key += ~(key << 11);
+    key ^=  (key >> 16);
+    return key;
+}
+#define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key)
+
+/* --- END OF HASH FUNCTIONS --- */
+
+/* Other convenient macros... */
+
+/*!
+  @abstract Type of the hash table.
+  @param  name  Name of the hash table [symbol]
+ */
+#define khash_t(name) kh_##name##_t
+
+/*! @function
+  @abstract     Initiate a hash table.
+  @param  name  Name of the hash table [symbol]
+  @return       Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_init(name) kh_init_##name()
+
+/*! @function
+  @abstract     Destroy a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_destroy(name, h) kh_destroy_##name(h)
+
+/*! @function
+  @abstract     Reset a hash table without deallocating memory.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_clear(name, h) kh_clear_##name(h)
+
+/*! @function
+  @abstract     Resize a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  s     New size [khint_t]
+ */
+#define kh_resize(name, h, s) kh_resize_##name(h, s)
+
+/*! @function
+  @abstract     Insert a key to the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @param  r     Extra return code: 0 if the key is present in the hash table;
+                1 if the bucket is empty (never used); 2 if the element in
+				the bucket has been deleted [int*]
+  @return       Iterator to the inserted element [khint_t]
+ */
+#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
+
+/*! @function
+  @abstract     Retrieve a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @return       Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
+ */
+#define kh_get(name, h, k) kh_get_##name(h, k)
+
+/*! @function
+  @abstract     Remove a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Iterator to the element to be deleted [khint_t]
+ */
+#define kh_del(name, h, k) kh_del_##name(h, k)
+
+/*! @function
+  @abstract     Test whether a bucket contains data.
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       1 if containing data; 0 otherwise [int]
+ */
+#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
+
+/*! @function
+  @abstract     Get key given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Key [type of keys]
+ */
+#define kh_key(h, x) ((h)->keys[x])
+
+/*! @function
+  @abstract     Get value given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Value [type of values]
+  @discussion   For hash sets, calling this results in segfault.
+ */
+#define kh_val(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Alias of kh_val()
+ */
+#define kh_value(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Get the start iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The start iterator [khint_t]
+ */
+#define kh_begin(h) (khint_t)(0)
+
+/*! @function
+  @abstract     Get the end iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The end iterator [khint_t]
+ */
+#define kh_end(h) ((h)->n_buckets)
+
+/*! @function
+  @abstract     Get the number of elements in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of elements in the hash table [khint_t]
+ */
+#define kh_size(h) ((h)->size)
+
+/*! @function
+  @abstract     Get the number of buckets in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of buckets in the hash table [khint_t]
+ */
+#define kh_n_buckets(h) ((h)->n_buckets)
+
+/*! @function
+  @abstract     Iterate over the entries in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  kvar  Variable to which key will be assigned
+  @param  vvar  Variable to which value will be assigned
+  @param  code  Block of code to execute
+ */
+#define kh_foreach(h, kvar, vvar, code) { khint_t __i;		\
+	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
+		if (!kh_exist(h,__i)) continue;						\
+		(kvar) = kh_key(h,__i);								\
+		(vvar) = kh_val(h,__i);								\
+		code;												\
+	} }
+
+/*! @function
+  @abstract     Iterate over the values in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  vvar  Variable to which value will be assigned
+  @param  code  Block of code to execute
+ */
+#define kh_foreach_value(h, vvar, code) { khint_t __i;		\
+	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
+		if (!kh_exist(h,__i)) continue;						\
+		(vvar) = kh_val(h,__i);								\
+		code;												\
+	} }
+
+/* More conenient interfaces */
+
+/*! @function
+  @abstract     Instantiate a hash set containing integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT(name)										\
+	KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT(name, khval_t)								\
+	KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT64(name)										\
+	KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT64(name, khval_t)								\
+	KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+
+typedef const char *kh_cstr_t;
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_STR(name)										\
+	KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_STR(name, khval_t)								\
+	KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+#endif /* __AC_KHASH_H */

kopen.c

@@ -0,0 +1,374 @@
+#include <stdio.h>
+#include <fcntl.h>
+#include <errno.h>
+#include <ctype.h>
+#include <unistd.h>
+#include <string.h>
+#include <stdlib.h>
+#include <signal.h>
+#include <sys/wait.h>
+#include <sys/types.h>
+#ifndef _WIN32
+#include <netdb.h>
+#include <arpa/inet.h>
+#include <sys/socket.h>
+#endif
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#ifdef _WIN32
+#define _KO_NO_NET
+#endif
+
+#ifndef _KO_NO_NET
+static int socket_wait(int fd, int is_read)
+{
+	fd_set fds, *fdr = 0, *fdw = 0;
+	struct timeval tv;
+	int ret;
+	tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
+	FD_ZERO(&fds);
+	FD_SET(fd, &fds);
+	if (is_read) fdr = &fds;
+	else fdw = &fds;
+	ret = select(fd+1, fdr, fdw, 0, &tv);
+	if (ret == -1) perror("select");
+	return ret;
+}
+
+static int socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
+
+	int on = 1, fd;
+	struct linger lng = { 0, 0 };
+	struct addrinfo hints, *res = 0;
+	memset(&hints, 0, sizeof(struct addrinfo));
+	hints.ai_family = AF_UNSPEC;
+	hints.ai_socktype = SOCK_STREAM;
+	if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
+	if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
+	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
+	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+	if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
+	freeaddrinfo(res);
+	return fd;
+#undef __err_connect
+}
+
+static int write_bytes(int fd, const char *buf, size_t len)
+{
+	ssize_t bytes;
+	do {
+		bytes = write(fd, buf, len);
+		if (bytes >= 0) {
+			len -= bytes;
+		} else if (errno != EAGAIN && errno != EWOULDBLOCK && errno != EINTR) {
+			return -1;
+		}
+	} while (len > 0);
+
+	return 0;
+}
+
+static int http_open(const char *fn)
+{
+	char *p, *proxy, *q, *http_host, *host, *port, *path, *buf;
+	int fd, ret, l;
+	ssize_t bytes = 0, bufsz = 0x10000;
+
+	/* parse URL; adapted from khttp_parse_url() in knetfile.c */
+	if (strstr(fn, "http://") != fn) return 0;
+	// set ->http_host
+	for (p = (char*)fn + 7; *p && *p != '/'; ++p);
+	l = p - fn - 7;
+	http_host = calloc(l + 1, 1);
+	strncpy(http_host, fn + 7, l);
+	http_host[l] = 0;
+	for (q = http_host; *q && *q != ':'; ++q);
+	if (*q == ':') *q++ = 0;
+	// get http_proxy
+	proxy = getenv("http_proxy");
+	// set host, port and path
+	if (proxy == 0) {
+		host = strdup(http_host); // when there is no proxy, server name is identical to http_host name.
+		port = strdup(*q? q : "80");
+		path = strdup(*p? p : "/");
+	} else {
+		host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
+		for (q = host; *q && *q != ':'; ++q);
+		if (*q == ':') *q++ = 0; 
+		port = strdup(*q? q : "80");
+		path = strdup(fn);
+	}
+
+	/* connect; adapted from khttp_connect() in knetfile.c */
+	l = 0;
+	fd = socket_connect(host, port);
+	buf = calloc(bufsz, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
+	l += snprintf(buf + l, bufsz, "GET %s HTTP/1.0\r\nHost: %s\r\n\r\n",
+				 path, http_host);
+	if (write_bytes(fd, buf, l) != 0) {
+		close(fd);
+		fd = -1;
+		goto out;
+	}
+	l = 0;
+ retry:
+	while (l < bufsz && (bytes = read(fd, buf + l, 1)) > 0) { // read HTTP header; FIXME: bad efficiency
+		if (buf[l] == '\n' && l >= 3)
+			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
+		++l;
+	}
+	if (bytes < 0 && (errno == EAGAIN || errno == EWOULDBLOCK || errno == EINTR)) goto retry;
+
+	buf[l] = 0;
+	if (bytes < 0 || l < 14) { // prematured header
+		close(fd);
+		fd = -1;
+		goto out;
+	}
+	ret = strtol(buf + 8, &p, 0); // HTTP return code
+	if (ret != 200) {
+		close(fd);
+		fd = -1;
+	}
+ out:
+	free(buf); free(http_host); free(host); free(port); free(path);
+	return fd;
+}
+
+typedef struct {
+	int max_response, ctrl_fd;
+	char *response;
+} ftpaux_t;
+
+static int kftp_get_response(ftpaux_t *aux)
+{
+	unsigned char c;
+	int n = 0;
+	char *p;
+	if (socket_wait(aux->ctrl_fd, 1) <= 0) return 0;
+	while (read(aux->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
+		if (n >= aux->max_response) {
+			aux->max_response = aux->max_response? aux->max_response<<1 : 256;
+			aux->response = realloc(aux->response, aux->max_response);
+		}
+		aux->response[n++] = c;
+		if (c == '\n') {
+			if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
+				&& aux->response[3] != '-') break;
+			n = 0;
+			continue;
+		}
+	}
+	if (n < 2) return -1;
+	aux->response[n-2] = 0;
+	return strtol(aux->response, &p, 0);
+}
+
+static int kftp_send_cmd(ftpaux_t *aux, const char *cmd, int is_get)
+{
+	if (socket_wait(aux->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
+	if (write_bytes(aux->ctrl_fd, cmd, strlen(cmd)) != 0) return -1;
+	return is_get? kftp_get_response(aux) : 0;
+}
+
+static int ftp_open(const char *fn)
+{
+	char *p, *host = 0, *port = 0, *retr = 0;
+	char host2[80], port2[10];
+	int v[6], l, fd = -1, ret, pasv_port, pasv_ip[4];
+	ftpaux_t aux;
+	
+	/* parse URL */
+	if (strstr(fn, "ftp://") != fn) return 0;
+	for (p = (char*)fn + 6; *p && *p != '/'; ++p);
+	if (*p != '/') return 0;
+	l = p - fn - 6;
+	port = strdup("21");
+	host = calloc(l + 1, 1);
+	strncpy(host, fn + 6, l);
+	retr = calloc(strlen(p) + 8, 1);
+	sprintf(retr, "RETR %s\r\n", p);
+	
+	/* connect to ctrl */
+	memset(&aux, 0, sizeof(ftpaux_t));
+	aux.ctrl_fd = socket_connect(host, port);
+	if (aux.ctrl_fd == -1) goto ftp_open_end; /* fail to connect ctrl */
+
+	/* connect to the data stream */
+	kftp_get_response(&aux);
+	kftp_send_cmd(&aux, "USER anonymous\r\n", 1);
+	kftp_send_cmd(&aux, "PASS kopen@\r\n", 1);
+	kftp_send_cmd(&aux, "TYPE I\r\n", 1);
+	kftp_send_cmd(&aux, "PASV\r\n", 1);
+	for (p = aux.response; *p && *p != '('; ++p);
+	if (*p != '(') goto ftp_open_end;
+	++p;
+	sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
+	memcpy(pasv_ip, v, 4 * sizeof(int));
+	pasv_port = (v[4]<<8&0xff00) + v[5];
+	kftp_send_cmd(&aux, retr, 0);
+	sprintf(host2, "%d.%d.%d.%d", pasv_ip[0], pasv_ip[1], pasv_ip[2], pasv_ip[3]);
+	sprintf(port2, "%d", pasv_port);
+	fd = socket_connect(host2, port2);
+	if (fd == -1) goto ftp_open_end;
+	ret = kftp_get_response(&aux);
+	if (ret != 150) {
+		close(fd);
+		fd = -1;
+	}
+	close(aux.ctrl_fd);
+
+ftp_open_end:
+	free(host); free(port); free(retr); free(aux.response);
+	return fd;
+}
+#endif /* !defined(_KO_NO_NET) */
+
+static char **cmd2argv(const char *cmd)
+{
+	int i, beg, end, argc;
+	char **argv, *str;
+	end = strlen(cmd);
+	for (i = end - 1; i >= 0; --i)
+		if (!isspace(cmd[i])) break;
+	end = i + 1;
+	for (beg = 0; beg < end; ++beg)
+		if (!isspace(cmd[beg])) break;
+	if (beg == end) return 0;
+	for (i = beg + 1, argc = 0; i < end; ++i)
+		if (isspace(cmd[i]) && !isspace(cmd[i-1]))
+			++argc;
+	argv = (char**)calloc(argc + 2, sizeof(void*));
+	argv[0] = str = (char*)calloc(end - beg + 1, 1);
+	strncpy(argv[0], cmd + beg, end - beg);
+	for (i = argc = 1; i < end - beg; ++i)
+		if (isspace(str[i])) str[i] = 0;
+		else if (str[i] && str[i-1] == 0) argv[argc++] = &str[i];
+	return argv;
+}
+
+#define KO_STDIN    1
+#define KO_FILE     2
+#define KO_PIPE     3
+#define KO_HTTP     4
+#define KO_FTP      5
+
+typedef struct {
+	int type, fd;
+	pid_t pid;
+} koaux_t;
+
+void *kopen(const char *fn, int *_fd)
+{
+	koaux_t *aux = 0;
+	*_fd = -1;
+	if (strstr(fn, "http://") == fn) {
+		aux = calloc(1, sizeof(koaux_t));
+		aux->type = KO_HTTP;
+		aux->fd = http_open(fn);
+	} else if (strstr(fn, "ftp://") == fn) {
+		aux = calloc(1, sizeof(koaux_t));
+		aux->type = KO_FTP;
+		aux->fd = ftp_open(fn);
+	} else if (strcmp(fn, "-") == 0) {
+		aux = calloc(1, sizeof(koaux_t));
+		aux->type = KO_STDIN;
+		aux->fd = STDIN_FILENO;
+	} else {
+		const char *p, *q;
+		for (p = fn; *p; ++p)
+			if (!isspace(*p)) break;
+		if (*p == '<') { // pipe open
+			int need_shell, pfd[2];
+			pid_t pid;
+			// a simple check to see if we need to invoke a shell; not always working
+			for (q = p + 1; *q; ++q)
+				if (ispunct(*q) && *q != '.' && *q != '_' && *q != '-' && *q != ':')
+					break;
+			need_shell = (*q != 0);
+			if (pipe(pfd) != 0) return 0;
+			pid = vfork();
+			if (pid == -1) { /* vfork() error */
+				close(pfd[0]); close(pfd[1]);
+				return 0;
+			}
+			if (pid == 0) { /* the child process */
+				char **argv; /* FIXME: I do not know if this will lead to a memory leak */
+				close(pfd[0]);
+				dup2(pfd[1], STDOUT_FILENO);
+				close(pfd[1]);
+				if (!need_shell) {
+					argv = cmd2argv(p + 1);
+					execvp(argv[0], argv);
+					free(argv[0]); free(argv);
+				} else execl("/bin/sh", "sh", "-c", p + 1, NULL);
+				exit(1);
+			} else { /* parent process */
+				close(pfd[1]);
+				aux = calloc(1, sizeof(koaux_t));
+				aux->type = KO_PIPE;
+				aux->fd = pfd[0];
+				aux->pid = pid;
+			}
+		} else {
+#ifdef _WIN32
+			*_fd = open(fn, O_RDONLY | O_BINARY);
+#else
+			*_fd = open(fn, O_RDONLY);
+#endif
+			if (*_fd >= 0) {
+				aux = calloc(1, sizeof(koaux_t));
+				aux->type = KO_FILE;
+				aux->fd = *_fd;
+			}
+		}
+	}
+	if (aux) *_fd = aux->fd;
+	return aux;
+}
+
+int kclose(void *a)
+{
+	koaux_t *aux = (koaux_t*)a;
+	if (aux->type == KO_PIPE) {
+		int status;
+		pid_t pid;
+		pid = waitpid(aux->pid, &status, WNOHANG);
+		if (pid != aux->pid) kill(aux->pid, 15);
+	}
+	free(aux);
+	return 0;
+}
+
+#ifdef _KO_MAIN
+#define BUF_SIZE 0x10000
+int main(int argc, char *argv[])
+{
+	void *x;
+	int l, fd;
+	unsigned char buf[BUF_SIZE];
+	FILE *fp;
+	if (argc == 1) {
+		fprintf(stderr, "Usage: kopen <file>\n");
+		return 1;
+	}
+	x = kopen(argv[1], &fd);
+	fp = fdopen(fd, "r");
+	if (fp == 0) {
+		fprintf(stderr, "ERROR: fail to open the input\n");
+		return 1;
+	}
+	do {
+		if ((l = fread(buf, 1, BUF_SIZE, fp)) != 0)
+			fwrite(buf, 1, l, stdout);
+	} while (l == BUF_SIZE);
+	fclose(fp);
+	kclose(x);
+	return 0;
+}
+#endif

kseq.h

@@ -0,0 +1,239 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Last Modified: 05MAR2012 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX   2
+
+#define __KS_TYPE(type_t)						\
+	typedef struct __kstream_t {				\
+		unsigned char *buf;						\
+		int begin, end, is_eof;					\
+		type_t f;								\
+	} kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize)								\
+	static inline kstream_t *ks_init(type_t f)						\
+	{																\
+		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
+		ks->f = f;													\
+		ks->buf = (unsigned char*)malloc(__bufsize);				\
+		return ks;													\
+	}																\
+	static inline void ks_destroy(kstream_t *ks)					\
+	{																\
+		if (ks) {													\
+			free(ks->buf);											\
+			free(ks);												\
+		}															\
+	}
+
+#define __KS_GETC(__read, __bufsize)						\
+	static inline int ks_getc(kstream_t *ks)				\
+	{														\
+		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
+		if (ks->begin >= ks->end) {							\
+			ks->begin = 0;									\
+			ks->end = __read(ks->f, ks->buf, __bufsize);	\
+			if (ks->end == 0) { ks->is_eof = 1; return -1;}	\
+		}													\
+		return (int)ks->buf[ks->begin++];					\
+	}
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize)								\
+	static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
+	{																	\
+		int gotany = 0;													\
+		if (dret) *dret = 0;											\
+		str->l = append? str->l : 0;									\
+		for (;;) {														\
+			int i;														\
+			if (ks->begin >= ks->end) {									\
+				if (!ks->is_eof) {										\
+					ks->begin = 0;										\
+					ks->end = __read(ks->f, ks->buf, __bufsize);		\
+					if (ks->end == 0) { ks->is_eof = 1; break; }		\
+				} else break;											\
+			}															\
+			if (delimiter == KS_SEP_LINE) { \
+				for (i = ks->begin; i < ks->end; ++i) \
+					if (ks->buf[i] == '\n') break; \
+			} else if (delimiter > KS_SEP_MAX) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (ks->buf[i] == delimiter) break;					\
+			} else if (delimiter == KS_SEP_SPACE) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i])) break;						\
+			} else if (delimiter == KS_SEP_TAB) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+			} else i = 0; /* never come to here! */						\
+			if (str->m - str->l < (size_t)(i - ks->begin + 1)) {		\
+				str->m = str->l + (i - ks->begin) + 1;					\
+				kroundup32(str->m);										\
+				str->s = (char*)realloc(str->s, str->m);				\
+			}															\
+			gotany = 1;													\
+			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+			str->l = str->l + (i - ks->begin);							\
+			ks->begin = i + 1;											\
+			if (i < ks->end) {											\
+				if (dret) *dret = ks->buf[i];							\
+				break;													\
+			}															\
+		}																\
+		if (!gotany && ks_eof(ks)) return -1;							\
+		if (str->s == 0) {												\
+			str->m = 1;													\
+			str->s = (char*)calloc(1, 1);								\
+		} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
+		str->s[str->l] = '\0';											\
+		return str->l;													\
+	} \
+	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+	__KS_TYPE(type_t)							\
+	__KS_BASIC(type_t, __bufsize)				\
+	__KS_GETC(__read, __bufsize)				\
+	__KS_GETUNTIL(__read, __bufsize)
+
+#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
+
+#define __KSEQ_BASIC(SCOPE, type_t)										\
+	SCOPE kseq_t *kseq_init(type_t fd)									\
+	{																	\
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
+		s->f = ks_init(fd);												\
+		return s;														\
+	}																	\
+	SCOPE void kseq_destroy(kseq_t *ks)									\
+	{																	\
+		if (!ks) return;												\
+		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
+		ks_destroy(ks->f);												\
+		free(ks);														\
+	}
+
+/* Return value:
+   >=0  length of the sequence (normal)
+   -1   end-of-file
+   -2   truncated quality string
+ */
+#define __KSEQ_READ(SCOPE) \
+	SCOPE int kseq_read(kseq_t *seq) \
+	{ \
+		int c; \
+		kstream_t *ks = seq->f; \
+		if (seq->last_char == 0) { /* then jump to the next header line */ \
+			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+			if (c == -1) return -1; /* end of file */ \
+			seq->last_char = c; \
+		} /* else: the first header char has been read in the previous call */ \
+		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
+		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
+		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
+			seq->seq.m = 256; \
+			seq->seq.s = (char*)malloc(seq->seq.m); \
+		} \
+		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+			if (c == '\n') continue; /* skip empty lines */ \
+			seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
+			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
+		} \
+		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
+		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
+			seq->seq.m = seq->seq.l + 2; \
+			kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
+			seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+		} \
+		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */ \
+		if (c != '+') return seq->seq.l; /* FASTA */ \
+		if (seq->qual.m < seq->seq.m) {	/* allocate memory for qual in case insufficient */ \
+			seq->qual.m = seq->seq.m; \
+			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+		} \
+		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+		if (c == -1) return -2; /* error: no quality string */ \
+		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+		seq->last_char = 0;	/* we have not come to the next header line */ \
+		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
+		return seq->seq.l; \
+	}
+
+#define __KSEQ_TYPE(type_t)						\
+	typedef struct {							\
+		kstring_t name, comment, seq, qual;		\
+		int last_char;							\
+		kstream_t *f;							\
+	} kseq_t;
+
+#define KSEQ_INIT2(SCOPE, type_t, __read)		\
+	KSTREAM_INIT(type_t, __read, 16384)			\
+	__KSEQ_TYPE(type_t)							\
+	__KSEQ_BASIC(SCOPE, type_t)					\
+	__KSEQ_READ(SCOPE)
+
+#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
+
+#define KSEQ_DECLARE(type_t) \
+	__KS_TYPE(type_t) \
+	__KSEQ_TYPE(type_t) \
+	extern kseq_t *kseq_init(type_t fd); \
+	void kseq_destroy(kseq_t *ks); \
+	int kseq_read(kseq_t *seq);
+
+#endif

ksort.h

@@ -0,0 +1,273 @@
+/* The MIT License
+
+   Copyright (c) 2008, by Attractive Chaos <attractivechaos@aol.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  2008-11-16 (0.1.4):
+
+    * Fixed a bug in introsort() that happens in rare cases.
+
+  2008-11-05 (0.1.3):
+
+    * Fixed a bug in introsort() for complex comparisons.
+
+	* Fixed a bug in mergesort(). The previous version is not stable.
+
+  2008-09-15 (0.1.2):
+
+	* Accelerated introsort. On my Mac (not on another Linux machine),
+	  my implementation is as fast as std::sort on random input.
+
+	* Added combsort and in introsort, switch to combsort if the
+	  recursion is too deep.
+
+  2008-09-13 (0.1.1):
+
+	* Added k-small algorithm
+
+  2008-09-05 (0.1.0):
+
+	* Initial version
+
+*/
+
+#ifndef AC_KSORT_H
+#define AC_KSORT_H
+
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+typedef struct {
+	void *left, *right;
+	int depth;
+} ks_isort_stack_t;
+
+#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
+
+#define KSORT_INIT(name, type_t, __sort_lt)								\
+	void ks_mergesort_##name(size_t n, type_t array[], type_t temp[])	\
+	{																	\
+		type_t *a2[2], *a, *b;											\
+		int curr, shift;												\
+																		\
+		a2[0] = array;													\
+		a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);	\
+		for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) {			\
+			a = a2[curr]; b = a2[1-curr];								\
+			if (shift == 0) {											\
+				type_t *p = b, *i, *eb = a + n;							\
+				for (i = a; i < eb; i += 2) {							\
+					if (i == eb - 1) *p++ = *i;							\
+					else {												\
+						if (__sort_lt(*(i+1), *i)) {					\
+							*p++ = *(i+1); *p++ = *i;					\
+						} else {										\
+							*p++ = *i; *p++ = *(i+1);					\
+						}												\
+					}													\
+				}														\
+			} else {													\
+				size_t i, step = 1ul<<shift;							\
+				for (i = 0; i < n; i += step<<1) {						\
+					type_t *p, *j, *k, *ea, *eb;						\
+					if (n < i + step) {									\
+						ea = a + n; eb = a;								\
+					} else {											\
+						ea = a + i + step;								\
+						eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
+					}													\
+					j = a + i; k = a + i + step; p = b + i;				\
+					while (j < ea && k < eb) {							\
+						if (__sort_lt(*k, *j)) *p++ = *k++;				\
+						else *p++ = *j++;								\
+					}													\
+					while (j < ea) *p++ = *j++;							\
+					while (k < eb) *p++ = *k++;							\
+				}														\
+			}															\
+			curr = 1 - curr;											\
+		}																\
+		if (curr == 1) {												\
+			type_t *p = a2[0], *i = a2[1], *eb = array + n;				\
+			for (; p < eb; ++i) *p++ = *i;								\
+		}																\
+		if (temp == 0) free(a2[1]);										\
+	}																	\
+	void ks_heapadjust_##name(size_t i, size_t n, type_t l[])			\
+	{																	\
+		size_t k = i;													\
+		type_t tmp = l[i];												\
+		while ((k = (k << 1) + 1) < n) {								\
+			if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k;				\
+			if (__sort_lt(l[k], tmp)) break;							\
+			l[i] = l[k]; i = k;											\
+		}																\
+		l[i] = tmp;														\
+	}																	\
+	void ks_heapmake_##name(size_t lsize, type_t l[])					\
+	{																	\
+		size_t i;														\
+		for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i)				\
+			ks_heapadjust_##name(i, lsize, l);							\
+	}																	\
+	void ks_heapsort_##name(size_t lsize, type_t l[])					\
+	{																	\
+		size_t i;														\
+		for (i = lsize - 1; i > 0; --i) {								\
+			type_t tmp;													\
+			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
+		}																\
+	}																	\
+	static inline void __ks_insertsort_##name(type_t *s, type_t *t)		\
+	{																	\
+		type_t *i, *j, swap_tmp;										\
+		for (i = s + 1; i < t; ++i)										\
+			for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {			\
+				swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;			\
+			}															\
+	}																	\
+	void ks_combsort_##name(size_t n, type_t a[])						\
+	{																	\
+		const double shrink_factor = 1.2473309501039786540366528676643; \
+		int do_swap;													\
+		size_t gap = n;													\
+		type_t tmp, *i, *j;												\
+		do {															\
+			if (gap > 2) {												\
+				gap = (size_t)(gap / shrink_factor);					\
+				if (gap == 9 || gap == 10) gap = 11;					\
+			}															\
+			do_swap = 0;												\
+			for (i = a; i < a + n - gap; ++i) {							\
+				j = i + gap;											\
+				if (__sort_lt(*j, *i)) {								\
+					tmp = *i; *i = *j; *j = tmp;						\
+					do_swap = 1;										\
+				}														\
+			}															\
+		} while (do_swap || gap > 2);									\
+		if (gap != 1) __ks_insertsort_##name(a, a + n);					\
+	}																	\
+	void ks_introsort_##name(size_t n, type_t a[])						\
+	{																	\
+		int d;															\
+		ks_isort_stack_t *top, *stack;									\
+		type_t rp, swap_tmp;											\
+		type_t *s, *t, *i, *j, *k;										\
+																		\
+		if (n < 1) return;												\
+		else if (n == 2) {												\
+			if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
+			return;														\
+		}																\
+		for (d = 2; 1ul<<d < n; ++d);									\
+		stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
+		top = stack; s = a; t = a + (n-1); d <<= 1;						\
+		while (1) {														\
+			if (s < t) {												\
+				if (--d == 0) {											\
+					ks_combsort_##name(t - s + 1, s);					\
+					t = s;												\
+					continue;											\
+				}														\
+				i = s; j = t; k = i + ((j-i)>>1) + 1;					\
+				if (__sort_lt(*k, *i)) {								\
+					if (__sort_lt(*k, *j)) k = j;						\
+				} else k = __sort_lt(*j, *i)? i : j;					\
+				rp = *k;												\
+				if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }	\
+				for (;;) {												\
+					do ++i; while (__sort_lt(*i, rp));					\
+					do --j; while (i <= j && __sort_lt(rp, *j));		\
+					if (j <= i) break;									\
+					swap_tmp = *i; *i = *j; *j = swap_tmp;				\
+				}														\
+				swap_tmp = *i; *i = *t; *t = swap_tmp;					\
+				if (i-s > t-i) {										\
+					if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
+					s = t-i > 16? i+1 : t;								\
+				} else {												\
+					if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
+					t = i-s > 16? i-1 : s;								\
+				}														\
+			} else {													\
+				if (top == stack) {										\
+					free(stack);										\
+					__ks_insertsort_##name(a, a+n);						\
+					return;												\
+				} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
+			}															\
+		}																\
+	}																	\
+	/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
+	/* 0 <= kk < n */													\
+	type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk)			\
+	{																	\
+		type_t *low, *high, *k, *ll, *hh, *mid;							\
+		low = arr; high = arr + n - 1; k = arr + kk;					\
+		for (;;) {														\
+			if (high <= low) return *k;									\
+			if (high == low + 1) {										\
+				if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+				return *k;												\
+			}															\
+			mid = low + (high - low) / 2;								\
+			if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
+			if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+			if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);	\
+			KSORT_SWAP(type_t, *mid, *(low+1));							\
+			ll = low + 1; hh = high;									\
+			for (;;) {													\
+				do ++ll; while (__sort_lt(*ll, *low));					\
+				do --hh; while (__sort_lt(*low, *hh));					\
+				if (hh < ll) break;										\
+				KSORT_SWAP(type_t, *ll, *hh);							\
+			}															\
+			KSORT_SWAP(type_t, *low, *hh);								\
+			if (hh <= k) low = ll;										\
+			if (hh >= k) high = hh - 1;									\
+		}																\
+	}
+
+#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
+#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
+#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
+#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
+#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
+#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
+#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
+
+#define ks_lt_generic(a, b) ((a) < (b))
+#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
+
+typedef const char *ksstr_t;
+
+#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
+#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
+
+#endif

kstring.c

@@ -0,0 +1,39 @@
+#include <stdarg.h>
+#include <stdio.h>
+#include "kstring.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+	va_list ap;
+	int l;
+	va_start(ap, fmt);
+	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+	va_end(ap);
+	if (l + 1 > s->m - s->l) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+		va_start(ap, fmt);
+		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+	}
+	va_end(ap);
+	s->l += l;
+	return l;
+}
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+	kstring_t *s;
+	s = (kstring_t*)calloc(1, sizeof(kstring_t));
+	ksprintf(s, "abcdefg: %d", 100);
+	printf("%s\n", s->s);
+	free(s);
+	return 0;
+}
+#endif

kstring.h

@@ -0,0 +1,115 @@
+#ifndef KSTRING_H
+#define KSTRING_H
+
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+static inline void ks_resize(kstring_t *s, size_t size)
+{
+	if (s->m < size) {
+		s->m = size;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+}
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
+{
+	if (s->l + l + 1 >= s->m) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	memcpy(s->s + s->l, p, l);
+	s->l += l;
+	s->s[s->l] = 0;
+	return l;
+}
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+	return kputsn(p, strlen(p), s);
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+	if (s->l + 1 >= s->m) {
+		s->m = s->l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	s->s[s->l++] = c;
+	s->s[s->l] = 0;
+	return c;
+}
+
+static inline int kputw(int c, kstring_t *s)
+{
+	char buf[16];
+	int l, x;
+	if (c == 0) return kputc('0', s);
+	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+	if (c < 0) buf[l++] = '-';
+	if (s->l + l + 1 >= s->m) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+static inline int kputuw(unsigned c, kstring_t *s)
+{
+	char buf[16];
+	int l, i;
+	unsigned x;
+	if (c == 0) return kputc('0', s);
+	for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+	if (s->l + l + 1 >= s->m) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+static inline int kputl(long c, kstring_t *s)
+{
+	char buf[32];
+	long l, x;
+	if (c == 0) return kputc('0', s);
+	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+	if (c < 0) buf[l++] = '-';
+	if (s->l + l + 1 >= s->m) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+int ksprintf(kstring_t *s, const char *fmt, ...);
+
+#endif

ksw.c

@@ -0,0 +1,749 @@
+/* The MIT License
+
+   Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <assert.h>
+#if defined __SSE2__
+#include <emmintrin.h>
+#elif defined __ARM_NEON
+#include "neon_sse.h"
+#else
+#include "scalar_sse.h"
+#endif
+#include "ksw.h"
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#ifdef __GNUC__
+#define LIKELY(x) __builtin_expect((x),1)
+#define UNLIKELY(x) __builtin_expect((x),0)
+#else
+#define LIKELY(x) (x)
+#define UNLIKELY(x) (x)
+#endif
+
+const kswr_t g_defr = { 0, -1, -1, -1, -1, -1, -1 };
+
+struct _kswq_t {
+	int qlen, slen;
+	uint8_t shift, mdiff, max, size;
+	__m128i *qp, *H0, *H1, *E, *Hmax;
+};
+
+/**
+ * Initialize the query data structure
+ *
+ * @param size   Number of bytes used to store a score; valid valures are 1 or 2
+ * @param qlen   Length of the query sequence
+ * @param query  Query sequence
+ * @param m      Size of the alphabet
+ * @param mat    Scoring matrix in a one-dimension array
+ *
+ * @return       Query data structure
+ */
+kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
+{
+	kswq_t *q;
+	int slen, a, tmp, p;
+
+	size = size > 1? 2 : 1;
+	p = 8 * (3 - size); // # values per __m128i
+	slen = (qlen + p - 1) / p; // segmented length
+	q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory
+	q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
+	q->H0 = q->qp + slen * m;
+	q->H1 = q->H0 + slen;
+	q->E  = q->H1 + slen;
+	q->Hmax = q->E + slen;
+	q->slen = slen; q->qlen = qlen; q->size = size;
+	// compute shift
+	tmp = m * m;
+	for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
+		if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
+		if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
+	}
+	q->max = q->mdiff;
+	q->shift = 256 - q->shift; // NB: q->shift is uint8_t
+	q->mdiff += q->shift; // this is the difference between the min and max scores
+	// An example: p=8, qlen=19, slen=3 and segmentation:
+	//  {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
+	if (size == 1) {
+		int8_t *t = (int8_t*)q->qp;
+		for (a = 0; a < m; ++a) {
+			int i, k, nlen = slen * p;
+			const int8_t *ma = mat + a * m;
+			for (i = 0; i < slen; ++i)
+				for (k = i; k < nlen; k += slen) // p iterations
+					*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
+		}
+	} else {
+		int16_t *t = (int16_t*)q->qp;
+		for (a = 0; a < m; ++a) {
+			int i, k, nlen = slen * p;
+			const int8_t *ma = mat + a * m;
+			for (i = 0; i < slen; ++i)
+				for (k = i; k < nlen; k += slen) // p iterations
+					*t++ = (k >= qlen? 0 : ma[query[k]]);
+		}
+	}
+	return q;
+}
+
+#if defined __ARM_NEON
+// This macro implicitly uses each function's `zero` local variable
+#define _mm_slli_si128(a, n) (vextq_u8(zero, (a), 16 - (n)))
+#endif
+
+kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
+{
+	int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
+	uint64_t *b;
+	__m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax;
+	kswr_t r;
+
+#if defined __SSE2__
+#define __max_16(ret, xx) do { \
+		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
+		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
+		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \
+		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \
+    	(ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
+	} while (0)
+
+// Given entries with arbitrary values, return whether they are all 0x00
+#define allzero_16(xx) (_mm_movemask_epi8(_mm_cmpeq_epi8((xx), zero)) == 0xffff)
+
+#elif defined __ARM_NEON
+#define __max_16(ret, xx) (ret) = vmaxvq_u8((xx))
+#define allzero_16(xx) (vmaxvq_u8((xx)) == 0)
+
+#else
+#define __max_16(ret, xx) (ret) = m128i_max_u8((xx))
+#define allzero_16(xx) (m128i_allzero((xx)))
+#endif
+
+	// initialization
+	r = g_defr;
+	minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
+	endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
+	m_b = n_b = 0; b = 0;
+	zero = _mm_set1_epi32(0);
+	oe_del = _mm_set1_epi8(_o_del + _e_del);
+	e_del = _mm_set1_epi8(_e_del);
+	oe_ins = _mm_set1_epi8(_o_ins + _e_ins);
+	e_ins = _mm_set1_epi8(_e_ins);
+	shift = _mm_set1_epi8(q->shift);
+	H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
+	slen = q->slen;
+	for (i = 0; i < slen; ++i) {
+		_mm_store_si128(E + i, zero);
+		_mm_store_si128(H0 + i, zero);
+		_mm_store_si128(Hmax + i, zero);
+	}
+	// the core loop
+	for (i = 0; i < tlen; ++i) {
+		int j, k, imax;
+		__m128i e, h, t, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
+		h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
+		h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
+		for (j = 0; LIKELY(j < slen); ++j) {
+			/* SW cells are computed in the following order:
+			 *   H(i,j)   = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
+			 *   E(i+1,j) = max{H(i,j)-q, E(i,j)-r}
+			 *   F(i,j+1) = max{H(i,j)-q, F(i,j)-r}
+			 */
+			// compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)
+			h = _mm_adds_epu8(h, _mm_load_si128(S + j));
+			h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
+			e = _mm_load_si128(E + j); // e=E'(i,j)
+			h = _mm_max_epu8(h, e);
+			h = _mm_max_epu8(h, f); // h=H'(i,j)
+			max = _mm_max_epu8(max, h); // set max
+			_mm_store_si128(H1 + j, h); // save to H'(i,j)
+			// now compute E'(i+1,j)
+			e = _mm_subs_epu8(e, e_del); // e=E'(i,j) - e_del
+			t = _mm_subs_epu8(h, oe_del); // h=H'(i,j) - o_del - e_del
+			e = _mm_max_epu8(e, t); // e=E'(i+1,j)
+			_mm_store_si128(E + j, e); // save to E'(i+1,j)
+			// now compute F'(i,j+1)
+			f = _mm_subs_epu8(f, e_ins);
+			t = _mm_subs_epu8(h, oe_ins); // h=H'(i,j) - o_ins - e_ins
+			f = _mm_max_epu8(f, t);
+			// get H'(i-1,j) and prepare for the next j
+			h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
+		}
+		// NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
+		for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
+			f = _mm_slli_si128(f, 1);
+			for (j = 0; LIKELY(j < slen); ++j) {
+				h = _mm_load_si128(H1 + j);
+				h = _mm_max_epu8(h, f); // h=H'(i,j)
+				_mm_store_si128(H1 + j, h);
+				h = _mm_subs_epu8(h, oe_ins);
+				f = _mm_subs_epu8(f, e_ins);
+				if (UNLIKELY(allzero_16(_mm_subs_epu8(f, h)))) goto end_loop16;
+			}
+		}
+end_loop16:
+		//int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");
+		__max_16(imax, max); // imax is the maximum number in max
+		if (imax >= minsc) { // write the b array; this condition adds branching unfornately
+			if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
+				if (n_b == m_b) {
+					m_b = m_b? m_b<<1 : 8;
+					b = (uint64_t*)realloc(b, 8 * m_b);
+				}
+				b[n_b++] = (uint64_t)imax<<32 | i;
+			} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
+		}
+		if (imax > gmax) {
+			gmax = imax; te = i; // te is the end position on the target
+			for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
+				_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
+			if (gmax + q->shift >= 255 || gmax >= endsc) break;
+		}
+		S = H1; H1 = H0; H0 = S; // swap H0 and H1
+	}
+	r.score = gmax + q->shift < 255? gmax : 255;
+	r.te = te;
+	if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
+		int max = -1, tmp, low, high, qlen = slen * 16;
+		uint8_t *t = (uint8_t*)Hmax;
+		for (i = 0; i < qlen; ++i, ++t)
+			if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;
+			else if ((int)*t == max && (tmp = i / 16 + i % 16 * slen) < r.qe) r.qe = tmp; 
+		//printf("%d,%d\n", max, gmax);
+		if (b) {
+			i = (r.score + q->max - 1) / q->max;
+			low = te - i; high = te + i;
+			for (i = 0; i < n_b; ++i) {
+				int e = (int32_t)b[i];
+				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
+					r.score2 = b[i]>>32, r.te2 = e;
+			}
+		}
+	}
+	free(b);
+	return r;
+}
+
+kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
+{
+	int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
+	uint64_t *b;
+	__m128i zero, oe_del, e_del, oe_ins, e_ins, *H0, *H1, *E, *Hmax;
+	kswr_t r;
+
+#if defined __SSE2__
+#define __max_8(ret, xx) do { \
+		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
+		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
+		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
+    	(ret) = _mm_extract_epi16((xx), 0); \
+	} while (0)
+
+// Given entries all either 0x0000 or 0xffff, return whether they are all 0x0000
+#define allzero_0f_8(xx) (!_mm_movemask_epi8((xx)))
+
+#elif defined __ARM_NEON
+#define __max_8(ret, xx) (ret) = vmaxvq_s16(vreinterpretq_s16_u8((xx)))
+#define allzero_0f_8(xx) (vmaxvq_u16(vreinterpretq_u16_u8((xx))) == 0)
+
+#else
+#define __max_8(ret, xx) (ret) = m128i_max_s16((xx))
+#define allzero_0f_8(xx) (m128i_allzero((xx)))
+#endif
+
+	// initialization
+	r = g_defr;
+	minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
+	endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
+	m_b = n_b = 0; b = 0;
+	zero = _mm_set1_epi32(0);
+	oe_del = _mm_set1_epi16(_o_del + _e_del);
+	e_del = _mm_set1_epi16(_e_del);
+	oe_ins = _mm_set1_epi16(_o_ins + _e_ins);
+	e_ins = _mm_set1_epi16(_e_ins);
+	H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
+	slen = q->slen;
+	for (i = 0; i < slen; ++i) {
+		_mm_store_si128(E + i, zero);
+		_mm_store_si128(H0 + i, zero);
+		_mm_store_si128(Hmax + i, zero);
+	}
+	// the core loop
+	for (i = 0; i < tlen; ++i) {
+		int j, k, imax;
+		__m128i e, t, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
+		h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
+		h = _mm_slli_si128(h, 2);
+		for (j = 0; LIKELY(j < slen); ++j) {
+			h = _mm_adds_epi16(h, _mm_load_si128(S++));
+			e = _mm_load_si128(E + j);
+			h = _mm_max_epi16(h, e);
+			h = _mm_max_epi16(h, f);
+			max = _mm_max_epi16(max, h);
+			_mm_store_si128(H1 + j, h);
+			e = _mm_subs_epu16(e, e_del);
+			t = _mm_subs_epu16(h, oe_del);
+			e = _mm_max_epi16(e, t);
+			_mm_store_si128(E + j, e);
+			f = _mm_subs_epu16(f, e_ins);
+			t = _mm_subs_epu16(h, oe_ins);
+			f = _mm_max_epi16(f, t);
+			h = _mm_load_si128(H0 + j);
+		}
+		for (k = 0; LIKELY(k < 16); ++k) {
+			f = _mm_slli_si128(f, 2);
+			for (j = 0; LIKELY(j < slen); ++j) {
+				h = _mm_load_si128(H1 + j);
+				h = _mm_max_epi16(h, f);
+				_mm_store_si128(H1 + j, h);
+				h = _mm_subs_epu16(h, oe_ins);
+				f = _mm_subs_epu16(f, e_ins);
+				if(UNLIKELY(allzero_0f_8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
+			}
+		}
+end_loop8:
+		__max_8(imax, max);
+		if (imax >= minsc) {
+			if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
+				if (n_b == m_b) {
+					m_b = m_b? m_b<<1 : 8;
+					b = (uint64_t*)realloc(b, 8 * m_b);
+				}
+				b[n_b++] = (uint64_t)imax<<32 | i;
+			} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
+		}
+		if (imax > gmax) {
+			gmax = imax; te = i;
+			for (j = 0; LIKELY(j < slen); ++j)
+				_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
+			if (gmax >= endsc) break;
+		}
+		S = H1; H1 = H0; H0 = S;
+	}
+	r.score = gmax; r.te = te;
+	{
+		int max = -1, tmp, low, high, qlen = slen * 8;
+		uint16_t *t = (uint16_t*)Hmax;
+		for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
+			if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
+			else if ((int)*t == max && (tmp = i / 8 + i % 8 * slen) < r.qe) r.qe = tmp; 
+		if (b) {
+			i = (r.score + q->max - 1) / q->max;
+			low = te - i; high = te + i;
+			for (i = 0; i < n_b; ++i) {
+				int e = (int32_t)b[i];
+				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
+					r.score2 = b[i]>>32, r.te2 = e;
+			}
+		}
+	}
+	free(b);
+	return r;
+}
+
+static inline void revseq(int l, uint8_t *s)
+{
+	int i, t;
+	for (i = 0; i < l>>1; ++i)
+		t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;
+}
+
+kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int xtra, kswq_t **qry)
+{
+	int size;
+	kswq_t *q;
+	kswr_t r, rr;
+	kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int, int, int);
+
+	q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
+	if (qry && *qry == 0) *qry = q;
+	func = q->size == 2? ksw_i16 : ksw_u8;
+	size = q->size;
+	r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);
+	if (qry == 0) free(q);
+	if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;
+	revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end
+	q = ksw_qinit(size, r.qe + 1, query, m, mat);
+	rr = func(q, tlen, target, o_del, e_del, o_ins, e_ins, KSW_XSTOP | r.score);
+	revseq(r.qe + 1, query); revseq(r.te + 1, target);
+	free(q);
+	if (r.score == rr.score)
+		r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;
+	return r;
+}
+
+kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)
+{
+	return ksw_align2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, xtra, qry);
+}
+
+/********************
+ *** SW extension ***
+ ********************/
+
+typedef struct {
+	int32_t h, e;
+} eh_t;
+
+int ksw_extend2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
+{
+	eh_t *eh; // score array
+	int8_t *qp; // query profile
+	int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
+	assert(h0 > 0);
+	// allocate memory
+	qp = malloc(qlen * m);
+	eh = calloc(qlen + 1, 8);
+	// generate the query profile
+	for (k = i = 0; k < m; ++k) {
+		const int8_t *p = &mat[k * m];
+		for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
+	}
+	// fill the first row
+	eh[0].h = h0; eh[1].h = h0 > oe_ins? h0 - oe_ins : 0;
+	for (j = 2; j <= qlen && eh[j-1].h > e_ins; ++j)
+		eh[j].h = eh[j-1].h - e_ins;
+	// adjust $w if it is too large
+	k = m * m;
+	for (i = 0, max = 0; i < k; ++i) // get the max score
+		max = max > mat[i]? max : mat[i];
+	max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
+	max_ins = max_ins > 1? max_ins : 1;
+	w = w < max_ins? w : max_ins;
+	max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
+	max_del = max_del > 1? max_del : 1;
+	w = w < max_del? w : max_del; // TODO: is this necessary?
+	// DP loop
+	max = h0, max_i = max_j = -1; max_ie = -1, gscore = -1;
+	max_off = 0;
+	beg = 0, end = qlen;
+	for (i = 0; LIKELY(i < tlen); ++i) {
+		int t, f = 0, h1, m = 0, mj = -1;
+		int8_t *q = &qp[target[i] * qlen];
+		// apply the band and the constraint (if provided)
+		if (beg < i - w) beg = i - w;
+		if (end > i + w + 1) end = i + w + 1;
+		if (end > qlen) end = qlen;
+		// compute the first column
+		if (beg == 0) {
+			h1 = h0 - (o_del + e_del * (i + 1));
+			if (h1 < 0) h1 = 0;
+		} else h1 = 0;
+		for (j = beg; LIKELY(j < end); ++j) {
+			// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
+			// Similar to SSE2-SW, cells are computed in the following order:
+			//   H(i,j)   = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
+			//   E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
+			//   F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
+			eh_t *p = &eh[j];
+			int h, M = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
+			p->h = h1;          // set H(i,j-1) for the next row
+			M = M? M + q[j] : 0;// separating H and M to disallow a cigar like "100M3I3D20M"
+			h = M > e? M : e;   // e and f are guaranteed to be non-negative, so h>=0 even if M<0
+			h = h > f? h : f;
+			h1 = h;             // save H(i,j) to h1 for the next column
+			mj = m > h? mj : j; // record the position where max score is achieved
+			m = m > h? m : h;   // m is stored at eh[mj+1]
+			t = M - oe_del;
+			t = t > 0? t : 0;
+			e -= e_del;
+			e = e > t? e : t;   // computed E(i+1,j)
+			p->e = e;           // save E(i+1,j) for the next row
+			t = M - oe_ins;
+			t = t > 0? t : 0;
+			f -= e_ins;
+			f = f > t? f : t;   // computed F(i,j+1)
+		}
+		eh[end].h = h1; eh[end].e = 0;
+		if (j == qlen) {
+			max_ie = gscore > h1? max_ie : i;
+			gscore = gscore > h1? gscore : h1;
+		}
+		if (m == 0) break;
+		if (m > max) {
+			max = m, max_i = i, max_j = mj;
+			max_off = max_off > abs(mj - i)? max_off : abs(mj - i);
+		} else if (zdrop > 0) {
+			if (i - max_i > mj - max_j) {
+				if (max - m - ((i - max_i) - (mj - max_j)) * e_del > zdrop) break;
+			} else {
+				if (max - m - ((mj - max_j) - (i - max_i)) * e_ins > zdrop) break;
+			}
+		}
+		// update beg and end for the next round
+		for (j = beg; LIKELY(j < end) && eh[j].h == 0 && eh[j].e == 0; ++j);
+		beg = j;
+		for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j);
+		end = j + 2 < qlen? j + 2 : qlen;
+		//beg = 0; end = qlen; // uncomment this line for debugging
+	}
+	free(eh); free(qp);
+	if (_qle) *_qle = max_j + 1;
+	if (_tle) *_tle = max_i + 1;
+	if (_gtle) *_gtle = max_ie + 1;
+	if (_gscore) *_gscore = gscore;
+	if (_max_off) *_max_off = max_off;
+	return max;
+}
+
+int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off)
+{
+	return ksw_extend2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off);
+}
+
+/********************
+ * Global alignment *
+ ********************/
+
+#define MINUS_INF -0x40000000
+
+static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
+{
+	if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
+		if (*n_cigar == *m_cigar) {
+			*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
+			cigar = realloc(cigar, (*m_cigar) << 2);
+		}
+		cigar[(*n_cigar)++] = len<<4 | op;
+	} else cigar[(*n_cigar)-1] += len<<4;
+	return cigar;
+}
+
+int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int *n_cigar_, uint32_t **cigar_)
+{
+	eh_t *eh;
+	int8_t *qp; // query profile
+	int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, score, n_col;
+	uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex
+	if (n_cigar_) *n_cigar_ = 0;
+	// allocate memory
+	n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
+	z = n_cigar_ && cigar_? malloc((long)n_col * tlen) : 0;
+	qp = malloc(qlen * m);
+	eh = calloc(qlen + 1, 8);
+	// generate the query profile
+	for (k = i = 0; k < m; ++k) {
+		const int8_t *p = &mat[k * m];
+		for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
+	}
+	// fill the first row
+	eh[0].h = 0; eh[0].e = MINUS_INF;
+	for (j = 1; j <= qlen && j <= w; ++j)
+		eh[j].h = -(o_ins + e_ins * j), eh[j].e = MINUS_INF;
+	for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band
+	// DP loop
+	for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop
+		int32_t f = MINUS_INF, h1, beg, end, t;
+		int8_t *q = &qp[target[i] * qlen];
+		beg = i > w? i - w : 0;
+		end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
+		h1 = beg == 0? -(o_del + e_del * (i + 1)) : MINUS_INF;
+		if (n_cigar_ && cigar_) {
+			uint8_t *zi = &z[(long)i * n_col];
+			for (j = beg; LIKELY(j < end); ++j) {
+				// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
+				// Cells are computed in the following order:
+				//   M(i,j)   = H(i-1,j-1) + S(i,j)
+				//   H(i,j)   = max{M(i,j), E(i,j), F(i,j)}
+				//   E(i+1,j) = max{M(i,j)-gapo, E(i,j)} - gape
+				//   F(i,j+1) = max{M(i,j)-gapo, F(i,j)} - gape
+				// We have to separate M(i,j); otherwise the direction may not be recorded correctly.
+				// However, a CIGAR like "10M3I3D10M" allowed by local() is disallowed by global().
+				// Such a CIGAR may occur, in theory, if mismatch_penalty > 2*gap_ext_penalty + 2*gap_open_penalty/k.
+				// In practice, this should happen very rarely given a reasonable scoring system.
+				eh_t *p = &eh[j];
+				int32_t h, m = p->h, e = p->e;
+				uint8_t d; // direction
+				p->h = h1;
+				m += q[j];
+				d = m >= e? 0 : 1;
+				h = m >= e? m : e;
+				d = h >= f? d : 2;
+				h = h >= f? h : f;
+				h1 = h;
+				t = m - oe_del;
+				e -= e_del;
+				d |= e > t? 1<<2 : 0;
+				e  = e > t? e    : t;
+				p->e = e;
+				t = m - oe_ins;
+				f -= e_ins;
+				d |= f > t? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two
+				f  = f > t? f    : t;
+				zi[j - beg] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
+			}
+		} else {
+			for (j = beg; LIKELY(j < end); ++j) {
+				eh_t *p = &eh[j];
+				int32_t h, m = p->h, e = p->e;
+				p->h = h1;
+				m += q[j];
+				h = m >= e? m : e;
+				h = h >= f? h : f;
+				h1 = h;
+				t = m - oe_del;
+				e -= e_del;
+				e  = e > t? e : t;
+				p->e = e;
+				t = m - oe_ins;
+				f -= e_ins;
+				f  = f > t? f : t;
+			}
+		}
+		eh[end].h = h1; eh[end].e = MINUS_INF;
+	}
+	score = eh[qlen].h;
+	if (n_cigar_ && cigar_) { // backtrack
+		int n_cigar = 0, m_cigar = 0, which = 0;
+		uint32_t *cigar = 0, tmp;
+		i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
+		while (i >= 0 && k >= 0) {
+			which = z[(long)i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
+			if (which == 0)      cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
+			else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
+			else                 cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
+		}
+		if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
+		if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
+		for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
+			tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
+		*n_cigar_ = n_cigar, *cigar_ = cigar;
+	}
+	free(eh); free(qp); free(z);
+	return score;
+}
+
+int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_)
+{
+	return ksw_global2(qlen, query, tlen, target, m, mat, gapo, gape, gapo, gape, w, n_cigar_, cigar_);
+}
+
+/*******************************************
+ * Main function (not compiled by default) *
+ *******************************************/
+
+#ifdef _KSW_MAIN
+
+#include <unistd.h>
+#include <stdio.h>
+#include <zlib.h>
+#include "kseq.h"
+KSEQ_INIT(gzFile, err_gzread)
+
+unsigned char seq_nt4_table[256] = {
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
+};
+
+int main(int argc, char *argv[])
+{
+	int c, sa = 1, sb = 3, i, j, k, forward_only = 0, max_rseq = 0;
+	int8_t mat[25];
+	int gapo = 5, gape = 2, minsc = 0, xtra = KSW_XSTART;
+	uint8_t *rseq = 0;
+	gzFile fpt, fpq;
+	kseq_t *kst, *ksq;
+
+	// parse command line
+	while ((c = getopt(argc, argv, "a:b:q:r:ft:1")) >= 0) {
+		switch (c) {
+			case 'a': sa = atoi(optarg); break;
+			case 'b': sb = atoi(optarg); break;
+			case 'q': gapo = atoi(optarg); break;
+			case 'r': gape = atoi(optarg); break;
+			case 't': minsc = atoi(optarg); break;
+			case 'f': forward_only = 1; break;
+			case '1': xtra |= KSW_XBYTE; break;
+		}
+	}
+	if (optind + 2 > argc) {
+		fprintf(stderr, "Usage: ksw [-1] [-f] [-a%d] [-b%d] [-q%d] [-r%d] [-t%d] <target.fa> <query.fa>\n", sa, sb, gapo, gape, minsc);
+		return 1;
+	}
+	if (minsc > 0xffff) minsc = 0xffff;
+	xtra |= KSW_XSUBO | minsc;
+	// initialize scoring matrix
+	for (i = k = 0; i < 4; ++i) {
+		for (j = 0; j < 4; ++j)
+			mat[k++] = i == j? sa : -sb;
+		mat[k++] = 0; // ambiguous base
+	}
+	for (j = 0; j < 5; ++j) mat[k++] = 0;
+	// open file
+	fpt = xzopen(argv[optind],   "r"); kst = kseq_init(fpt);
+	fpq = xzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
+	// all-pair alignment
+	while (kseq_read(ksq) > 0) {
+		kswq_t *q[2] = {0, 0};
+		kswr_t r;
+		for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
+		if (!forward_only) { // reverse
+			if ((int)ksq->seq.m > max_rseq) {
+				max_rseq = ksq->seq.m;
+				rseq = (uint8_t*)realloc(rseq, max_rseq);
+			}
+			for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j)
+				rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];
+		}
+		gzrewind(fpt); kseq_rewind(kst);
+		while (kseq_read(kst) > 0) {
+			for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
+			r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);
+			if (r.score >= minsc)
+				err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
+			if (rseq) {
+				r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);
+				if (r.score >= minsc)
+					err_printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
+			}
+		}
+		free(q[0]); free(q[1]);
+	}
+	free(rseq);
+	kseq_destroy(kst); err_gzclose(fpt);
+	kseq_destroy(ksq); err_gzclose(fpq);
+	return 0;
+}
+#endif

ksw.h

@@ -0,0 +1,114 @@
+#ifndef __AC_KSW_H
+#define __AC_KSW_H
+
+#include <stdint.h>
+
+#define KSW_XBYTE  0x10000
+#define KSW_XSTOP  0x20000
+#define KSW_XSUBO  0x40000
+#define KSW_XSTART 0x80000
+
+struct _kswq_t;
+typedef struct _kswq_t kswq_t;
+
+typedef struct {
+	int score; // best score
+	int te, qe; // target end and query end
+	int score2, te2; // second best score and ending position on the target
+	int tb, qb; // target start and query start
+} kswr_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	/**
+	 * Aligning two sequences
+	 *
+	 * @param qlen    length of the query sequence (typically <tlen)
+	 * @param query   query sequence with 0 <= query[i] < m
+	 * @param tlen    length of the target sequence
+	 * @param target  target sequence
+	 * @param m       number of residue types
+	 * @param mat     m*m scoring matrix in one-dimension array
+	 * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
+	 * @param gape    gap extension penalty
+	 * @param xtra    extra information (see below)
+	 * @param qry     query profile (see below)
+	 *
+	 * @return        alignment information in a struct; unset values to -1
+	 *
+	 * When xtra==0, ksw_align() uses a signed two-byte integer to store a
+	 * score and only finds the best score and the end positions. The 2nd best
+	 * score or the start positions are not attempted. The default behavior can
+	 * be tuned by setting KSW_X* flags:
+	 *
+	 *   KSW_XBYTE:  use an unsigned byte to store a score. If overflow occurs,
+	 *               kswr_t::score will be set to 255
+	 *
+	 *   KSW_XSUBO:  track the 2nd best score and the ending position on the
+	 *               target if the 2nd best is higher than (xtra&0xffff)
+	 *
+	 *   KSW_XSTOP:  stop if the maximum score is above (xtra&0xffff)
+	 *
+	 *   KSW_XSTART: find the start positions
+	 *
+	 * When *qry==NULL, ksw_align() will compute and allocate the query profile
+	 * and when the function returns, *qry will point to the profile, which can
+	 * be deallocated simply by free(). If one query is aligned against multiple
+	 * target sequences, *qry should be set to NULL during the first call and
+	 * freed after the last call. Note that qry can equal 0. In this case, the
+	 * query profile will be deallocated in ksw_align().
+	 */
+	kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
+	kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int xtra, kswq_t **qry);
+
+	/**
+	 * Banded global alignment
+	 *
+	 * @param qlen    query length
+	 * @param query   query sequence with 0 <= query[i] < m
+	 * @param tlen    target length
+	 * @param target  target sequence with 0 <= target[i] < m
+	 * @param m       number of residue types
+	 * @param mat     m*m scoring mattrix in one-dimension array
+	 * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
+	 * @param gape    gap extension penalty
+	 * @param w       band width
+	 * @param n_cigar (out) number of CIGAR elements
+	 * @param cigar   (out) BAM-encoded CIGAR; caller need to deallocate with free()
+	 *
+	 * @return        score of the alignment
+	 */
+	int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar);
+	int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int *n_cigar, uint32_t **cigar);
+
+	/**
+	 * Extend alignment
+	 *
+	 * The routine aligns $query and $target, assuming their upstream sequences,
+	 * which are not provided, have been aligned with score $h0. In return,
+	 * region [0,*qle) on the query and [0,*tle) on the target sequences are
+	 * aligned together. If *gscore>=0, *gscore keeps the best score such that
+	 * the entire query sequence is aligned; *gtle keeps the position on the
+	 * target where *gscore is achieved. Returning *gscore and *gtle helps the
+	 * caller to decide whether an end-to-end hit or a partial hit is preferred.
+	 *
+	 * The first 9 parameters are identical to those in ksw_global()
+	 *
+	 * @param h0      alignment score of upstream sequences
+	 * @param _qle    (out) length of the query in the alignment
+	 * @param _tle    (out) length of the target in the alignment
+	 * @param _gtle   (out) length of the target if query is fully aligned
+	 * @param _gscore (out) score of the best end-to-end alignment; negative if not found
+	 *
+	 * @return        best semi-local alignment score
+	 */
+	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
+	int ksw_extend2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

kthread.c

@@ -0,0 +1,147 @@
+#include <pthread.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include <limits.h>
+
+/************
+ * kt_for() *
+ ************/
+
+struct kt_for_t;
+
+typedef struct {
+	struct kt_for_t *t;
+	long i;
+} ktf_worker_t;
+
+typedef struct kt_for_t {
+	int n_threads;
+	long n;
+	ktf_worker_t *w;
+	void (*func)(void*,long,int);
+	void *data;
+} kt_for_t;
+
+static inline long steal_work(kt_for_t *t)
+{
+	int i, min_i = -1;
+	long k, min = LONG_MAX;
+	for (i = 0; i < t->n_threads; ++i)
+		if (min > t->w[i].i) min = t->w[i].i, min_i = i;
+	k = __sync_fetch_and_add(&t->w[min_i].i, t->n_threads);
+	return k >= t->n? -1 : k;
+}
+
+static void *ktf_worker(void *data)
+{
+	ktf_worker_t *w = (ktf_worker_t*)data;
+	long i;
+	for (;;) {
+		i = __sync_fetch_and_add(&w->i, w->t->n_threads);
+		if (i >= w->t->n) break;
+		w->t->func(w->t->data, i, w - w->t->w);
+	}
+	while ((i = steal_work(w->t)) >= 0)
+		w->t->func(w->t->data, i, w - w->t->w);
+	pthread_exit(0);
+}
+
+void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n)
+{
+	int i;
+	kt_for_t t;
+	pthread_t *tid;
+	t.func = func, t.data = data, t.n_threads = n_threads, t.n = n;
+	t.w = (ktf_worker_t*)alloca(n_threads * sizeof(ktf_worker_t));
+	tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
+	for (i = 0; i < n_threads; ++i)
+		t.w[i].t = &t, t.w[i].i = i;
+	for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktf_worker, &t.w[i]);
+	for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
+}
+
+/*****************
+ * kt_pipeline() *
+ *****************/
+
+struct ktp_t;
+
+typedef struct {
+	struct ktp_t *pl;
+	int64_t index;
+	int step;
+	void *data;
+} ktp_worker_t;
+
+typedef struct ktp_t {
+	void *shared;
+	void *(*func)(void*, int, void*);
+	int64_t index;
+	int n_workers, n_steps;
+	ktp_worker_t *workers;
+	pthread_mutex_t mutex;
+	pthread_cond_t cv;
+} ktp_t;
+
+static void *ktp_worker(void *data)
+{
+	ktp_worker_t *w = (ktp_worker_t*)data;
+	ktp_t *p = w->pl;
+	while (w->step < p->n_steps) {
+		// test whether we can kick off the job with this worker
+		pthread_mutex_lock(&p->mutex);
+		for (;;) {
+			int i;
+			// test whether another worker is doing the same step
+			for (i = 0; i < p->n_workers; ++i) {
+				if (w == &p->workers[i]) continue; // ignore itself
+				if (p->workers[i].step <= w->step && p->workers[i].index < w->index)
+					break;
+			}
+			if (i == p->n_workers) break; // no workers with smaller indices are doing w->step or the previous steps
+			pthread_cond_wait(&p->cv, &p->mutex);
+		}
+		pthread_mutex_unlock(&p->mutex);
+
+		// working on w->step
+		w->data = p->func(p->shared, w->step, w->step? w->data : 0); // for the first step, input is NULL
+
+		// update step and let other workers know
+		pthread_mutex_lock(&p->mutex);
+		w->step = w->step == p->n_steps - 1 || w->data? (w->step + 1) % p->n_steps : p->n_steps;
+		if (w->step == 0) w->index = p->index++;
+		pthread_cond_broadcast(&p->cv);
+		pthread_mutex_unlock(&p->mutex);
+	}
+	pthread_exit(0);
+}
+
+void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_data, int n_steps)
+{
+	ktp_t aux;
+	pthread_t *tid;
+	int i;
+
+	if (n_threads < 1) n_threads = 1;
+	aux.n_workers = n_threads;
+	aux.n_steps = n_steps;
+	aux.func = func;
+	aux.shared = shared_data;
+	aux.index = 0;
+	pthread_mutex_init(&aux.mutex, 0);
+	pthread_cond_init(&aux.cv, 0);
+
+	aux.workers = (ktp_worker_t*)alloca(n_threads * sizeof(ktp_worker_t));
+	for (i = 0; i < n_threads; ++i) {
+		ktp_worker_t *w = &aux.workers[i];
+		w->step = 0; w->pl = &aux; w->data = 0;
+		w->index = aux.index++;
+	}
+
+	tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
+	for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktp_worker, &aux.workers[i]);
+	for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
+
+	pthread_mutex_destroy(&aux.mutex);
+	pthread_cond_destroy(&aux.cv);
+}

kvec.h

@@ -0,0 +1,94 @@
+/* The MIT License
+
+   Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  An example:
+
+#include "kvec.h"
+int main() {
+	kvec_t(int) array;
+	kv_init(array);
+	kv_push(int, array, 10); // append
+	kv_a(int, array, 20) = 5; // dynamic
+	kv_A(array, 20) = 4; // static
+	kv_destroy(array);
+	return 0;
+}
+*/
+
+/*
+  2008-09-22 (0.1.0):
+
+	* The initial version.
+
+*/
+
+#ifndef AC_KVEC_H
+#define AC_KVEC_H
+
+#include <stdlib.h>
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+
+#define kvec_t(type) struct { size_t n, m; type *a; }
+#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
+#define kv_destroy(v) free((v).a)
+#define kv_A(v, i) ((v).a[(i)])
+#define kv_pop(v) ((v).a[--(v).n])
+#define kv_size(v) ((v).n)
+#define kv_max(v) ((v).m)
+
+#define kv_resize(type, v, s)  ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
+
+#define kv_copy(type, v1, v0) do {							\
+		if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n);	\
+		(v1).n = (v0).n;									\
+		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n);		\
+	} while (0)												\
+
+#define kv_push(type, v, x) do {									\
+		if ((v).n == (v).m) {										\
+			(v).m = (v).m? (v).m<<1 : 2;							\
+			(v).a = (type*)realloc((v).a, sizeof(type) * (v).m); \
+		}															\
+		(v).a[(v).n++] = (x);										\
+	} while (0)
+
+#define kv_pushp(type, v) ((((v).n == (v).m)?							\
+						   ((v).m = ((v).m? (v).m<<1 : 2),				\
+							(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0)	\
+						   : 0), &(v).a[(v).n++])
+
+#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
+						  ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
+						   (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
+						  : (v).n <= (size_t)(i)? (v).n = (i) + 1 \
+						  : 0), (v).a[(i)])
+
+#endif

main.c

@@ -0,0 +1,130 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#include <stdio.h>
+#include <string.h>
+#include "kstring.h"
+#include "utils.h"
+
+#ifndef PACKAGE_VERSION
+#define PACKAGE_VERSION "0.7.17-r1198-dirty"
+#endif
+
+int bwa_fa2pac(int argc, char *argv[]);
+int bwa_pac2bwt(int argc, char *argv[]);
+int bwa_bwtupdate(int argc, char *argv[]);
+int bwa_bwt2sa(int argc, char *argv[]);
+int bwa_index(int argc, char *argv[]);
+int bwt_bwtgen_main(int argc, char *argv[]);
+
+int bwa_aln(int argc, char *argv[]);
+int bwa_sai2sam_se(int argc, char *argv[]);
+int bwa_sai2sam_pe(int argc, char *argv[]);
+
+int bwa_bwtsw2(int argc, char *argv[]);
+
+int main_fastmap(int argc, char *argv[]);
+int main_mem(int argc, char *argv[]);
+int main_shm(int argc, char *argv[]);
+
+int main_pemerge(int argc, char *argv[]);
+int main_maxk(int argc, char *argv[]);
+	
+static int usage()
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
+	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+	fprintf(stderr, "Contact: Heng Li <hli@ds.dfci.harvard.edu>\n\n");
+	fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
+	fprintf(stderr, "Command: index         index sequences in the FASTA format\n");
+	fprintf(stderr, "         mem           BWA-MEM algorithm\n");
+	fprintf(stderr, "         fastmap       identify super-maximal exact matches\n");
+	fprintf(stderr, "         pemerge       merge overlapping paired ends (EXPERIMENTAL)\n");
+	fprintf(stderr, "         aln           gapped/ungapped alignment\n");
+	fprintf(stderr, "         samse         generate alignment (single ended)\n");
+	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
+	fprintf(stderr, "         bwasw         BWA-SW for long queries (DEPRECATED)\n");
+	fprintf(stderr, "\n");
+	fprintf(stderr, "         shm           manage indices in shared memory\n");
+	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
+	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
+	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
+	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
+	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
+	fprintf(stderr, "\n");
+	fprintf(stderr,
+"Note: To use BWA, you need to first index the genome with `bwa index'.\n"
+"      There are three alignment algorithms in BWA: `mem', `bwasw', and\n"
+"      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'\n"
+"      first. Please `man ./bwa.1' for the manual.\n\n");
+	return 1;
+}
+
+int main(int argc, char *argv[])
+{
+	extern char *bwa_pg;
+	int i, ret;
+	double t_real;
+	kstring_t pg = {0,0,0};
+	t_real = realtime();
+	ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
+	for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
+	bwa_pg = pg.s;
+	if (argc < 2) return usage();
+	if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
+	else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
+	else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
+	else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
+	else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
+	else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
+	else if (strcmp(argv[1], "shm") == 0) ret = main_shm(argc-1, argv+1);
+	else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
+	else if (strcmp(argv[1], "maxk") == 0) ret = main_maxk(argc-1, argv+1);
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	err_fflush(stdout);
+	err_fclose(stdout);
+	if (ret == 0) {
+		fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
+		fprintf(stderr, "[%s] CMD:", __func__);
+		for (i = 0; i < argc; ++i)
+			fprintf(stderr, " %s", argv[i]);
+		fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
+	}
+	free(bwa_pg);
+	return ret;
+}

malloc_wrap.c

@@ -0,0 +1,57 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#ifdef USE_MALLOC_WRAPPERS
+/* Don't wrap ourselves */
+#  undef USE_MALLOC_WRAPPERS
+#endif
+#include "malloc_wrap.h"
+
+void *wrap_calloc(size_t nmemb, size_t size,
+				  const char *file, unsigned int line, const char *func) {
+	void *p = calloc(nmemb, size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
+				func, nmemb * size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+void *wrap_malloc(size_t size,
+				  const char *file, unsigned int line, const char *func) {
+	void *p = malloc(size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
+				func, size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+void *wrap_realloc(void *ptr, size_t size,
+				   const char *file, unsigned int line, const char *func) {
+	void *p = realloc(ptr, size);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
+				func, size, file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}
+
+char *wrap_strdup(const char *s,
+				  const char *file, unsigned int line, const char *func) {
+	char *p = strdup(s);
+	if (NULL == p) {
+		fprintf(stderr,
+				"[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
+				func, strlen(s), file, line, strerror(errno));
+		exit(EXIT_FAILURE);
+	}
+	return p;
+}

malloc_wrap.h

@@ -0,0 +1,47 @@
+#ifndef MALLOC_WRAP_H
+#define MALLOC_WRAP_H
+
+#include <stdlib.h>  /* Avoid breaking the usual definitions */
+#include <string.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void *wrap_calloc(size_t nmemb, size_t size,
+					  const char *file, unsigned int line, const char *func);
+	void *wrap_malloc(size_t size,
+					  const char *file, unsigned int line, const char *func);
+	void *wrap_realloc(void *ptr, size_t size,
+					   const char *file, unsigned int line, const char *func);
+	char *wrap_strdup(const char *s,
+					  const char *file, unsigned int line, const char *func);
+
+#ifdef __cplusplus
+}
+#endif
+
+#ifdef USE_MALLOC_WRAPPERS
+#  ifdef calloc
+#    undef calloc
+#  endif
+#  define calloc(n, s)  wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
+
+#  ifdef malloc
+#    undef malloc
+#  endif
+#  define malloc(s)     wrap_malloc( (s),      __FILE__, __LINE__, __func__)
+
+#  ifdef realloc
+#    undef realloc
+#  endif
+#  define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
+
+#  ifdef strdup
+#    undef strdup
+#  endif
+#  define strdup(s)     wrap_strdup( (s),      __FILE__, __LINE__, __func__)
+
+#endif /* USE_MALLOC_WRAPPERS */
+
+#endif /* MALLOC_WRAP_H */

maxk.c

@@ -0,0 +1,67 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <limits.h>
+#include <string.h>
+#include <unistd.h>
+#include "bwa.h"
+#include "bwamem.h"
+#include "kseq.h"
+KSEQ_DECLARE(gzFile)
+
+int main_maxk(int argc, char *argv[])
+{
+	int i, c, self = 0, max_len = 0;
+	uint8_t *cnt = 0;
+	uint64_t hist[256];
+	bwt_t *bwt;
+	kseq_t *ks;
+	smem_i *itr;
+	gzFile fp;
+
+	while ((c = getopt(argc, argv, "s")) >= 0) {
+		if (c == 's') self = 1;
+	}
+	if (optind + 2 > argc) {
+		fprintf(stderr, "Usage: bwa maxk [-s] <index.prefix> <seq.fa>\n");
+		return 1;
+	}
+	fp = strcmp(argv[optind+1], "-")? gzopen(argv[optind+1], "rb") : gzdopen(fileno(stdin), "rb");
+	ks = kseq_init(fp);
+	bwt = bwt_restore_bwt(argv[optind]);
+	itr = smem_itr_init(bwt);
+	if (self) smem_config(itr, 2, INT_MAX, 0);
+	memset(hist, 0, 8 * 256);
+
+	while (kseq_read(ks) >= 0) {
+		const bwtintv_v *a;
+		if (ks->seq.l > max_len) {
+			max_len = ks->seq.l;
+			kroundup32(max_len);
+			cnt = realloc(cnt, max_len);
+		}
+		memset(cnt, 0, ks->seq.l);
+		for (i = 0; i < ks->seq.l; ++i)
+			ks->seq.s[i] = nst_nt4_table[(int)ks->seq.s[i]];
+		smem_set_query(itr, ks->seq.l, (uint8_t*)ks->seq.s);
+		while ((a = smem_next(itr)) != 0) {
+			for (i = 0; i < a->n; ++i) {
+				bwtintv_t *p = &a->a[i];
+				int j, l, start = p->info>>32, end = (uint32_t)p->info;
+				l = end - start < 255? end - start : 255;
+				for (j = start; j < end; ++j)
+					cnt[j] = cnt[j] > l? cnt[j] : l;
+			}
+		}
+		for (i = 0; i < ks->seq.l; ++i) ++hist[cnt[i]];
+	}
+	for (i = 0; i < 256; ++i)
+		printf("%d\t%lld\n", i, (long long)hist[i]);
+	free(cnt);
+
+	smem_itr_destroy(itr);
+	bwt_destroy(bwt);
+	kseq_destroy(ks);
+	gzclose(fp);
+	return 0;
+}

neon_sse.h

@@ -0,0 +1,33 @@
+#ifndef NEON_SSE_H
+#define NEON_SSE_H
+
+#include <arm_neon.h>
+
+typedef uint8x16_t __m128i;
+
+static inline __m128i _mm_load_si128(const __m128i *ptr) { return vld1q_u8((const uint8_t *) ptr); }
+static inline __m128i _mm_set1_epi32(int n) { return vreinterpretq_u8_s32(vdupq_n_s32(n)); }
+static inline void _mm_store_si128(__m128i *ptr, __m128i a) { vst1q_u8((uint8_t *) ptr, a); }
+
+static inline __m128i _mm_adds_epu8(__m128i a, __m128i b) { return vqaddq_u8(a, b); }
+static inline __m128i _mm_max_epu8(__m128i a, __m128i b) { return vmaxq_u8(a, b); }
+static inline __m128i _mm_set1_epi8(int8_t n) { return vreinterpretq_u8_s8(vdupq_n_s8(n)); }
+static inline __m128i _mm_subs_epu8(__m128i a, __m128i b) { return vqsubq_u8(a, b); }
+
+#define M128I(a)  vreinterpretq_u8_s16((a))
+#define UM128I(a) vreinterpretq_u8_u16((a))
+#define S16(a)    vreinterpretq_s16_u8((a))
+#define U16(a)    vreinterpretq_u16_u8((a))
+
+static inline __m128i _mm_adds_epi16(__m128i a, __m128i b) { return M128I(vqaddq_s16(S16(a), S16(b))); }
+static inline __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) { return UM128I(vcgtq_s16(S16(a), S16(b))); }
+static inline __m128i _mm_max_epi16(__m128i a, __m128i b) { return M128I(vmaxq_s16(S16(a), S16(b))); }
+static inline __m128i _mm_set1_epi16(int16_t n) { return vreinterpretq_u8_s16(vdupq_n_s16(n)); }
+static inline __m128i _mm_subs_epu16(__m128i a, __m128i b) { return UM128I(vqsubq_u16(U16(a), U16(b))); }
+
+#undef M128I
+#undef UM128I
+#undef S16
+#undef U16
+
+#endif

pemerge.c

@@ -0,0 +1,291 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <zlib.h>
+#include <pthread.h>
+#include <errno.h>
+#include "ksw.h"
+#include "kseq.h"
+#include "kstring.h"
+#include "bwa.h"
+#include "utils.h"
+KSEQ_DECLARE(gzFile)
+
+#ifdef USE_MALLOC_WRAPPERS
+#  include "malloc_wrap.h"
+#endif
+
+#define MAX_SCORE_RATIO 0.9f
+#define MAX_ERR 8
+
+static const char *err_msg[MAX_ERR+1] = {
+	"successful merges",
+	"low-scoring pairs",
+	"pairs where the best SW alignment is not an overlap (long left end)",
+	"pairs where the best SW alignment is not an overlap (long right end)",
+	"pairs with large 2nd best SW score",
+	"pairs with gapped overlap",
+	"pairs where the end-to-end alignment is inconsistent with SW",
+	"pairs potentially with tandem overlaps",
+	"pairs with high sum of errors"
+};
+
+typedef struct {
+	int a, b, q, r, w;
+	int q_def, q_thres;
+	int T;
+	int chunk_size;
+	int n_threads;
+	int flag; // bit 1: print merged; 2: print unmerged
+	int8_t mat[25];
+} pem_opt_t;
+
+pem_opt_t *pem_opt_init()
+{
+	pem_opt_t *opt;
+	opt = calloc(1, sizeof(pem_opt_t));
+	opt->a = 5; opt->b = 4; opt->q = 2, opt->r = 17; opt->w = 20;
+	opt->T = opt->a * 10;
+	opt->q_def = 20;
+	opt->q_thres = 70;
+	opt->chunk_size = 10000000;
+	opt->n_threads = 1;
+	opt->flag = 3;
+	bwa_fill_scmat(opt->a, opt->b, opt->mat);
+	return opt;
+}
+
+int bwa_pemerge(const pem_opt_t *opt, bseq1_t x[2])
+{
+	uint8_t *s[2], *q[2], *seq, *qual;
+	int i, xtra, l, l_seq, sum_q, ret = 0;
+	kswr_t r;
+
+	s[0] = malloc(x[0].l_seq); q[0] = malloc(x[0].l_seq);
+	s[1] = malloc(x[1].l_seq); q[1] = malloc(x[1].l_seq);
+	for (i = 0; i < x[0].l_seq; ++i) {
+		int c = x[0].seq[i];
+		s[0][i] = c < 0 || c > 127? 4 : c <= 4? c : nst_nt4_table[c];
+		q[0][i] = x[0].qual? x[0].qual[i] - 33 : opt->q_def;
+	}
+	for (i = 0; i < x[1].l_seq; ++i) {
+		int c = x[1].seq[x[1].l_seq - 1 - i];
+		c = c < 0 || c > 127? 4 : c < 4? c : nst_nt4_table[c];
+		s[1][i] = c < 4? 3 - c : 4;
+		q[1][i] = x[1].qual? x[1].qual[x[1].l_seq - 1 - i] - 33 : opt->q_def;
+	}
+
+	xtra = KSW_XSTART | KSW_XSUBO;
+	r = ksw_align(x[1].l_seq, s[1], x[0].l_seq, s[0], 5, opt->mat, opt->q, opt->r, xtra, 0);
+	++r.qe; ++r.te; // change to the half-close-half-open coordinates
+
+	if (r.score < opt->T) { ret = -1; goto pem_ret; } // poor alignment
+	if (r.tb < r.qb) { ret = -2; goto pem_ret; } // no enough space for the left end
+	if (x[0].l_seq - r.te > x[1].l_seq - r.qe) { ret = -3; goto pem_ret; } // no enough space for the right end
+	if ((double)r.score2 / r.score >= MAX_SCORE_RATIO) { ret = -4; goto pem_ret; } // the second best score is too large
+	if (r.qe - r.qb != r.te - r.tb) { ret = -5; goto pem_ret; } // we do not allow gaps
+
+	{ // test tandem match; O(n^2)
+		int max_m, max_m2, min_l, max_l, max_l2;
+		max_m = max_m2 = 0; max_l = max_l2 = 0;
+		min_l = x[0].l_seq < x[1].l_seq? x[0].l_seq : x[1].l_seq;
+		for (l = 1; l < min_l; ++l) {
+			int m = 0, o = x[0].l_seq - l;
+			uint8_t *s0o = &s[0][o], *s1 = s[1];
+			for (i = 0; i < l; ++i) // TODO: in principle, this can be done with SSE2. It is the bottleneck!
+				m += opt->mat[(s1[i]<<2) + s1[i] + s0o[i]]; // equivalent to s[1][i]*5 + s[0][o+i]
+			if (m > max_m) max_m2 = max_m, max_m = m, max_l2 = max_l, max_l = l;
+			else if (m > max_m2) max_m2 = m, max_l2 = l;
+		}
+		if (max_m < opt->T || max_l != x[0].l_seq - (r.tb - r.qb)) { ret = -6; goto pem_ret; }
+		if (max_l2 < max_l && max_m2 >= opt->T && (double)(max_m2 + (max_l - max_l2) * opt->a) / max_m >= MAX_SCORE_RATIO) {
+			ret = -7; goto pem_ret;
+		}
+		if (max_l2 > max_l && (double)max_m2 / max_m >= MAX_SCORE_RATIO) { ret = -7; goto pem_ret; }
+	}
+
+	l = x[0].l_seq - (r.tb - r.qb); // length to merge
+	l_seq = x[0].l_seq + x[1].l_seq - l;
+	seq = malloc(l_seq + 1);
+	qual = malloc(l_seq + 1);
+	memcpy(seq,  s[0], x[0].l_seq); memcpy(seq  + x[0].l_seq, &s[1][l], x[1].l_seq - l);
+	memcpy(qual, q[0], x[0].l_seq); memcpy(qual + x[0].l_seq, &q[1][l], x[1].l_seq - l);
+	for (i = 0, sum_q = 0; i < l; ++i) {
+		int k = x[0].l_seq - l + i;
+		if (s[0][k] == 4) { // ambiguous
+			seq[k]  = s[1][i];
+			qual[k] = q[1][i];
+		} else if (s[1][i] == 4) { // do nothing
+		} else if (s[0][k] == s[1][i]) {
+			qual[k] = qual[k] > q[1][i]? qual[k] : q[1][i];
+		} else { // s[0][k] != s[1][i] and neither is N
+			int qq = q[0][k] < q[1][i]? q[0][k] : q[1][i];
+			sum_q += qq >= 3? qq<<1 : 1;
+			seq[k]  = q[0][k] > q[1][i]? s[0][k] : s[1][i];
+			qual[k] = abs((int)q[0][k] - (int)q[1][i]);
+		}
+	}
+	if (sum_q>>1 > opt->q_thres) { // too many mismatches
+		free(seq); free(qual);
+		ret = -8; goto pem_ret;
+	}
+
+	for (i = 0; i < l_seq; ++i) seq[i] = "ACGTN"[(int)seq[i]], qual[i] += 33;
+	seq[l_seq] = qual[l_seq] = 0;
+
+	free(x[1].name); free(x[1].seq); free(x[1].qual); free(x[1].comment);
+	memset(&x[1], 0, sizeof(bseq1_t));
+	free(x[0].seq); free(x[0].qual);
+	x[0].l_seq = l_seq; x[0].seq = (char*)seq; x[0].qual = (char*)qual;
+
+pem_ret:
+	free(s[0]); free(s[1]); free(q[0]); free(q[1]);
+	return ret;
+}
+
+static inline void print_bseq(const bseq1_t *s, int rn)
+{
+	err_putchar(s->qual? '@' : '>');
+	err_fputs(s->name, stdout);
+	if (rn == 1 || rn == 2) {
+		err_putchar('/'); err_putchar('0' + rn); err_putchar('\n');
+	} else err_puts(" merged");
+	err_puts(s->seq);
+	if (s->qual) {
+		err_puts("+"); err_puts(s->qual);
+	}
+}
+
+typedef struct {
+	int n, start;
+	bseq1_t *seqs;
+	int64_t cnt[MAX_ERR+1];
+	const pem_opt_t *opt;
+} worker_t;
+
+void *worker(void *data)
+{
+	worker_t *w = (worker_t*)data;
+	int i;
+	for (i = w->start; i < w->n>>1; i += w->opt->n_threads)
+		++w->cnt[-bwa_pemerge(w->opt, &w->seqs[i<<1])];
+	return 0;
+}
+
+static void process_seqs(const pem_opt_t *opt, int n_, bseq1_t *seqs, int64_t cnt[MAX_ERR+1])
+{
+	int i, j, n = n_>>1<<1;
+	worker_t *w;
+
+	w = calloc(opt->n_threads, sizeof(worker_t));
+	for (i = 0; i < opt->n_threads; ++i) {
+		worker_t *p = &w[i];
+		p->start = i; p->n = n;
+		p->opt = opt;
+		p->seqs = seqs;
+	}
+	if (opt->n_threads == 1) {
+		worker(w);
+	} else {
+		pthread_t *tid;
+		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
+		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker, &w[i]);
+		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
+		free(tid);
+	}
+	for (i = 0; i < opt->n_threads; ++i) {
+		worker_t *p = &w[i];
+		for (j = 0; j <= MAX_ERR; ++j) cnt[j] += p->cnt[j];
+	}
+	free(w);
+	for (i = 0; i < n>>1; ++i) {
+		if (seqs[i<<1|1].l_seq != 0) {
+			if (opt->flag&2) {
+				print_bseq(&seqs[i<<1|0], 1);
+				print_bseq(&seqs[i<<1|1], 2);
+			}
+		} else if (opt->flag&1)
+			print_bseq(&seqs[i<<1|0], 0);
+	}
+	for (i = 0; i < n; ++i) {
+		bseq1_t *s = &seqs[i];
+		free(s->name); free(s->seq); free(s->qual); free(s->comment);
+	}
+}
+
+int main_pemerge(int argc, char *argv[])
+{
+	int c, flag = 0, i, n, min_ovlp = 10;
+	int64_t cnt[MAX_ERR+1];
+	bseq1_t *bseq;
+	gzFile fp, fp2 = 0;
+	kseq_t *ks, *ks2 = 0;
+	pem_opt_t *opt;
+
+	opt = pem_opt_init();
+	while ((c = getopt(argc, argv, "muQ:t:T:")) >= 0) {
+		if (c == 'm') flag |= 1;
+		else if (c == 'u') flag |= 2;
+		else if (c == 'Q') opt->q_thres = atoi(optarg);
+		else if (c == 't') opt->n_threads = atoi(optarg);
+		else if (c == 'T') min_ovlp = atoi(optarg);
+		else return 1;
+	}
+	if (flag == 0) flag = 3;
+	opt->flag = flag;
+	opt->T = opt->a * min_ovlp;
+
+	if (optind == argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa pemerge [-mu] <read1.fq> [read2.fq]\n\n");
+		fprintf(stderr, "Options: -m       output merged reads only\n");
+		fprintf(stderr, "         -u       output unmerged reads only\n");
+		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "         -T INT   minimum end overlap [%d]\n", min_ovlp);
+		fprintf(stderr, "         -Q INT   max sum of errors [%d]\n", opt->q_thres);
+		fprintf(stderr, "\n");
+		free(opt);
+		return 1;
+	}
+
+	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+	if (NULL == fp) {
+		fprintf(stderr, "Couldn't open %s : %s\n",
+				strcmp(argv[optind], "-") ? argv[optind] : "stdin",
+				errno ? strerror(errno) : "Out of memory");
+		exit(EXIT_FAILURE);
+	}
+	ks = kseq_init(fp);
+	if (optind + 1 < argc) {
+		fp2 = strcmp(argv[optind+1], "-")? gzopen(argv[optind+1], "r") : gzdopen(fileno(stdin), "r");
+		if (NULL == fp) {
+			fprintf(stderr, "Couldn't open %s : %s\n",
+					strcmp(argv[optind+1], "-") ? argv[optind+1] : "stdin",
+					errno ? strerror(errno) : "Out of memory");
+			exit(EXIT_FAILURE);
+		}
+		ks2 = kseq_init(fp2);
+	}
+
+	memset(cnt, 0, 8 * (MAX_ERR+1));
+	while ((bseq = bseq_read(opt->n_threads * opt->chunk_size, &n, ks, ks2)) != 0) {
+		process_seqs(opt, n, bseq, cnt);
+		free(bseq);
+	}
+
+	fprintf(stderr, "%12ld %s\n", (long)cnt[0], err_msg[0]);
+	for (i = 1; i <= MAX_ERR; ++i)
+		fprintf(stderr, "%12ld %s\n", (long)cnt[i], err_msg[i]);
+	kseq_destroy(ks);
+	err_gzclose(fp);
+	if (ks2) {
+		kseq_destroy(ks2);
+		err_gzclose(fp2);
+	}
+	free(opt);
+
+	err_fflush(stdout);
+
+	return 0;
+}

qualfa2fq.pl

@@ -0,0 +1,27 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
+
+my ($fhs, $fhq, $q);
+open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
+open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
+
+$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
+while (<$fhs>) {
+  $q = <$fhq>;
+  print "\@$_";
+  $/ = ">";
+  $_ = <$fhs>; $q = <$fhq>;
+  chomp; chomp($q);
+  $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
+  print $_, "+\n";
+  for (my $i = 0; $i < length($q); $i += 60) {
+	print substr($q, $i, 60), "\n";
+  }
+  $/ = "\n";
+}
+
+close($fhs); close($fhq);

rle.c

@@ -0,0 +1,191 @@
+#include <string.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include "rle.h"
+
+const uint8_t rle_auxtab[8] = { 0x01, 0x11, 0x21, 0x31, 0x03, 0x13, 0x07, 0x17 };
+
+// insert symbol $a after $x symbols in $str; marginal counts added to $cnt; returns the size increase
+int rle_insert_cached(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6], int *beg, int64_t bc[6])
+{
+	uint16_t *nptr = (uint16_t*)block;
+	int diff;
+
+	block += 2; // skip the first 2 counting bytes
+	if (*nptr == 0) {
+		memset(cnt, 0, 48);
+		diff = rle_enc1(block, a, rl);
+	} else {
+		uint8_t *p, *end = block + *nptr, *q;
+		int64_t pre, z, l = 0, tot, beg_l;
+		int c = -1, n_bytes = 0, n_bytes2, t = 0;
+		uint8_t tmp[24];
+		beg_l = bc[0] + bc[1] + bc[2] + bc[3] + bc[4] + bc[5];
+		tot   = ec[0] + ec[1] + ec[2] + ec[3] + ec[4] + ec[5];
+		if (x < beg_l) {
+			beg_l = 0, *beg = 0;
+			memset(bc, 0, 48);
+		}
+		if (x == beg_l) {
+			p = q = block + (*beg); z = beg_l;
+			memcpy(cnt, bc, 48);
+		} else if (x - beg_l <= ((tot-beg_l)>>1) + ((tot-beg_l)>>3)) { // forward
+			z = beg_l; p = block + (*beg);
+			memcpy(cnt, bc, 48);
+			while (z < x) {
+				rle_dec1(p, c, l);
+				z += l; cnt[c] += l;
+			}
+			for (q = p - 1; *q>>6 == 2; --q);
+		} else { // backward
+			memcpy(cnt, ec, 48);
+			z = tot; p = end;
+			while (z >= x) {
+				--p;
+				if (*p>>6 != 2) {
+					l |= *p>>7? (int64_t)rle_auxtab[*p>>3&7]>>4 << t : *p>>3;
+					z -= l; cnt[*p&7] -= l;
+					l = 0; t = 0;
+				} else {
+					l |= (*p&0x3fL) << t;
+					t += 6;
+				}
+			}
+			q = p;
+			rle_dec1(p, c, l);
+			z += l; cnt[c] += l;
+		}
+		*beg = q - block;
+		memcpy(bc, cnt, 48);
+		bc[c] -= l;
+		n_bytes = p - q;
+		if (x == z && a != c && p < end) { // then try the next run
+			int tc;
+			int64_t tl;
+			q = p;
+			rle_dec1(q, tc, tl);
+			if (a == tc)
+				c = tc, n_bytes = q - p, l = tl, z += l, p = q, cnt[tc] += tl;
+		}
+		if (z != x) cnt[c] -= z - x;
+		pre = x - (z - l); p -= n_bytes;
+		if (a == c) { // insert to the same run
+			n_bytes2 = rle_enc1(tmp, c, l + rl);
+		} else if (x == z) { // at the end; append to the existing run
+			p += n_bytes; n_bytes = 0;
+			n_bytes2 = rle_enc1(tmp, a, rl);
+		} else { // break the current run
+			n_bytes2 = rle_enc1(tmp, c, pre);
+			n_bytes2 += rle_enc1(tmp + n_bytes2, a, rl);
+			n_bytes2 += rle_enc1(tmp + n_bytes2, c, l - pre);
+		}
+		if (n_bytes != n_bytes2 && end != p + n_bytes) // size changed
+			memmove(p + n_bytes2, p + n_bytes, end - p - n_bytes);
+		memcpy(p, tmp, n_bytes2);
+		diff = n_bytes2 - n_bytes;
+	}
+	return (*nptr += diff);
+}
+
+int rle_insert(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6])
+{
+	int beg = 0;
+	int64_t bc[6];
+	memset(bc, 0, 48);
+	return rle_insert_cached(block, x, a, rl, cnt, ec, &beg, bc);
+}
+
+void rle_split(uint8_t *block, uint8_t *new_block)
+{
+	int n = *(uint16_t*)block;
+	uint8_t *end = block + 2 + n, *q = block + 2 + (n>>1);
+	while (*q>>6 == 2) --q;
+	memcpy(new_block + 2, q, end - q);
+	*(uint16_t*)new_block = end - q;
+	*(uint16_t*)block = q - block - 2;
+}
+
+void rle_count(const uint8_t *block, int64_t cnt[6])
+{
+	const uint8_t *q = block + 2, *end = q + *(uint16_t*)block;
+	while (q < end) {
+		int c;
+		int64_t l;
+		rle_dec1(q, c, l);
+		cnt[c] += l;
+	}
+}
+
+void rle_print(const uint8_t *block, int expand)
+{
+	const uint16_t *p = (const uint16_t*)block;
+	const uint8_t *q = block + 2, *end = block + 2 + *p;
+	while (q < end) {
+		int c;
+		int64_t l, x;
+		rle_dec1(q, c, l);
+		if (expand) for (x = 0; x < l; ++x) putchar("$ACGTN"[c]);
+		else printf("%c%ld", "$ACGTN"[c], (long)l);
+	}
+	putchar('\n');
+}
+
+void rle_rank2a(const uint8_t *block, int64_t x, int64_t y, int64_t *cx, int64_t *cy, const int64_t ec[6])
+{
+	int a;
+	int64_t tot, cnt[6];
+	const uint8_t *p;
+
+	y = y >= x? y : x;
+	tot = ec[0] + ec[1] + ec[2] + ec[3] + ec[4] + ec[5];
+	if (tot == 0) return;
+	if (x <= (tot - y) + (tot>>3)) {
+		int c = 0;
+		int64_t l, z = 0;
+		memset(cnt, 0, 48);
+		p = block + 2;
+		while (z < x) {
+			rle_dec1(p, c, l);
+			z += l; cnt[c] += l;
+		}
+		for (a = 0; a != 6; ++a) cx[a] += cnt[a];
+		cx[c] -= z - x;
+		if (cy) {
+			while (z < y) {
+				rle_dec1(p, c, l);
+				z += l; cnt[c] += l;
+			}
+			for (a = 0; a != 6; ++a) cy[a] += cnt[a];
+			cy[c] -= z - y;
+		}
+	} else {
+#define move_backward(_x) \
+		while (z >= (_x)) { \
+			--p; \
+			if (*p>>6 != 2) { \
+				l |= *p>>7? (int64_t)rle_auxtab[*p>>3&7]>>4 << t : *p>>3; \
+				z -= l; cnt[*p&7] -= l; \
+				l = 0; t = 0; \
+			} else { \
+				l |= (*p&0x3fL) << t; \
+				t += 6; \
+			} \
+		} \
+
+		int t = 0;
+		int64_t l = 0, z = tot;
+		memcpy(cnt, ec, 48);
+		p = block + 2 + *(const uint16_t*)block;
+		if (cy) {
+			move_backward(y)
+			for (a = 0; a != 6; ++a) cy[a] += cnt[a];
+			cy[*p&7] += y - z;
+		}
+		move_backward(x)
+		for (a = 0; a != 6; ++a) cx[a] += cnt[a];
+		cx[*p&7] += x - z;
+
+#undef move_backward
+	}
+}

rle.h

@@ -0,0 +1,77 @@
+#ifndef RLE6_H_
+#define RLE6_H_
+
+#include <stdint.h>
+
+#ifdef __GNUC__
+#define LIKELY(x) __builtin_expect((x),1)
+#else
+#define LIKELY(x) (x)
+#endif
+#ifdef __cplusplus
+
+extern "C" {
+#endif
+
+	int rle_insert_cached(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t ec[6], int *beg, int64_t bc[6]);
+	int rle_insert(uint8_t *block, int64_t x, int a, int64_t rl, int64_t cnt[6], const int64_t end_cnt[6]);
+	void rle_split(uint8_t *block, uint8_t *new_block);
+	void rle_count(const uint8_t *block, int64_t cnt[6]);
+	void rle_rank2a(const uint8_t *block, int64_t x, int64_t y, int64_t *cx, int64_t *cy, const int64_t ec[6]);
+	#define rle_rank1a(block, x, cx, ec) rle_rank2a(block, x, -1, cx, 0, ec)
+
+	void rle_print(const uint8_t *block, int expand);
+
+#ifdef __cplusplus
+}
+#endif
+
+/******************
+ *** 43+3 codec ***
+ ******************/
+
+extern const uint8_t rle_auxtab[8];
+
+#define RLE_MIN_SPACE 18
+#define rle_nptr(block) ((uint16_t*)(block))
+
+// decode one run (c,l) and move the pointer p
+#define rle_dec1(p, c, l) do { \
+		(c) = *(p) & 7; \
+		if (LIKELY((*(p)&0x80) == 0)) { \
+			(l) = *(p)++ >> 3; \
+		} else if (LIKELY(*(p)>>5 == 6)) { \
+			(l) = (*(p)&0x18L)<<3L | ((p)[1]&0x3fL); \
+			(p) += 2; \
+		} else { \
+			int n = ((*(p)&0x10) >> 2) + 4; \
+			(l) = *(p)++ >> 3 & 1; \
+			while (--n) (l) = ((l)<<6) | (*(p)++&0x3fL); \
+		} \
+	} while (0)
+
+static inline int rle_enc1(uint8_t *p, int c, int64_t l)
+{
+	if (l < 1LL<<4) {
+		*p = l << 3 | c;
+		return 1;
+	} else if (l < 1LL<<8) {
+		*p = 0xC0 | l >> 6 << 3 | c;
+		p[1] = 0x80 | (l & 0x3f);
+		return 2;
+	} else if (l < 1LL<<19) {
+		*p = 0xE0 | l >> 18 << 3 | c;
+		p[1] = 0x80 | (l >> 12 & 0x3f);
+		p[2] = 0x80 | (l >> 6 & 0x3f);
+		p[3] = 0x80 | (l & 0x3f);
+		return 4;
+	} else {
+		int i, shift = 36;
+		*p = 0xF0 | l >> 42 << 3 | c;
+		for (i = 1; i < 8; ++i, shift -= 6)
+			p[i] = 0x80 | (l>>shift & 0x3f);
+		return 8;
+	}
+}
+
+#endif

rope.c

@@ -0,0 +1,318 @@
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <stdio.h>
+#include <zlib.h>
+#include "rle.h"
+#include "rope.h"
+
+/*******************
+ *** Memory Pool ***
+ *******************/
+
+#define MP_CHUNK_SIZE 0x100000 // 1MB per chunk
+
+typedef struct { // memory pool for fast and compact memory allocation (no free)
+	int size, i, n_elems;
+	int64_t top, max;
+	uint8_t **mem;
+} mempool_t;
+
+static mempool_t *mp_init(int size)
+{
+	mempool_t *mp;
+	mp = calloc(1, sizeof(mempool_t));
+	mp->size = size;
+	mp->i = mp->n_elems = MP_CHUNK_SIZE / size;
+	mp->top = -1;
+	return mp;
+}
+
+static void mp_destroy(mempool_t *mp)
+{
+	int64_t i;
+	for (i = 0; i <= mp->top; ++i) free(mp->mem[i]);
+	free(mp->mem); free(mp);
+}
+
+static inline void *mp_alloc(mempool_t *mp)
+{
+	if (mp->i == mp->n_elems) {
+		if (++mp->top == mp->max) {
+			mp->max = mp->max? mp->max<<1 : 1;
+			mp->mem = realloc(mp->mem, sizeof(void*) * mp->max);
+		}
+		mp->mem[mp->top] = calloc(mp->n_elems, mp->size);
+		mp->i = 0;
+	}
+	return mp->mem[mp->top] + (mp->i++) * mp->size;
+}
+
+/***************
+ *** B+ rope ***
+ ***************/
+
+rope_t *rope_init(int max_nodes, int block_len)
+{
+	rope_t *rope;
+	rope = calloc(1, sizeof(rope_t));
+	if (block_len < 32) block_len = 32;
+	rope->max_nodes = (max_nodes+ 1)>>1<<1;
+	rope->block_len = (block_len + 7) >> 3 << 3;
+	rope->node = mp_init(sizeof(rpnode_t) * rope->max_nodes);
+	rope->leaf = mp_init(rope->block_len);
+	rope->root = mp_alloc(rope->node);
+	rope->root->n = 1;
+	rope->root->is_bottom = 1;
+	rope->root->p = mp_alloc(rope->leaf);
+	return rope;
+}
+
+void rope_destroy(rope_t *rope)
+{
+	mp_destroy(rope->node);
+	mp_destroy(rope->leaf);
+	free(rope);
+}
+
+static inline rpnode_t *split_node(rope_t *rope, rpnode_t *u, rpnode_t *v)
+{ // split $v's child. $u is the first node in the bucket. $v and $u are in the same bucket. IMPORTANT: there is always enough room in $u
+	int j, i = v - u;
+	rpnode_t *w; // $w is the sibling of $v
+	if (u == 0) { // only happens at the root; add a new root
+		u = v = mp_alloc(rope->node);
+		v->n = 1; v->p = rope->root; // the new root has the old root as the only child
+		memcpy(v->c, rope->c, 48);
+		for (j = 0; j < 6; ++j) v->l += v->c[j];
+		rope->root = v;
+	}
+	if (i != u->n - 1) // then make room for a new node
+		memmove(v + 2, v + 1, sizeof(rpnode_t) * (u->n - i - 1));
+	++u->n; w = v + 1;
+	memset(w, 0, sizeof(rpnode_t));
+	w->p = mp_alloc(u->is_bottom? rope->leaf : rope->node);
+	if (u->is_bottom) { // we are at the bottom level; $v->p is a string instead of a node
+		uint8_t *p = (uint8_t*)v->p, *q = (uint8_t*)w->p;
+		rle_split(p, q);
+		rle_count(q, w->c);
+	} else { // $v->p is a node, not a string
+		rpnode_t *p = v->p, *q = w->p; // $v and $w are siblings and thus $p and $q are cousins
+		p->n -= rope->max_nodes>>1;
+		memcpy(q, p + p->n, sizeof(rpnode_t) * (rope->max_nodes>>1));
+		q->n = rope->max_nodes>>1; // NB: this line must below memcpy() as $q->n and $q->is_bottom are modified by memcpy()
+		q->is_bottom = p->is_bottom;
+		for (i = 0; i < q->n; ++i)
+			for (j = 0; j < 6; ++j)
+				w->c[j] += q[i].c[j];
+	}
+	for (j = 0; j < 6; ++j) // compute $w->l and update $v->c
+		w->l += w->c[j], v->c[j] -= w->c[j];
+	v->l -= w->l; // update $v->c
+	return v;
+}
+
+int64_t rope_insert_run(rope_t *rope, int64_t x, int a, int64_t rl, rpcache_t *cache)
+{ // insert $a after $x symbols in $rope and the returns rank(a, x)
+	rpnode_t *u = 0, *v = 0, *p = rope->root; // $v is the parent of $p; $u and $v are at the same level and $u is the first node in the bucket
+	int64_t y = 0, z = 0, cnt[6];
+	int n_runs;
+	do { // top-down update. Searching and node splitting are done together in one pass.
+		if (p->n == rope->max_nodes) { // node is full; split
+			v = split_node(rope, u, v); // $v points to the parent of $p; when a new root is added, $v points to the root
+			if (y + v->l < x) // if $v is not long enough after the split, we need to move both $p and its parent $v
+				y += v->l, z += v->c[a], ++v, p = v->p;
+		}
+		u = p;
+		if (v && x - y > v->l>>1) { // then search backwardly for the right node to descend
+			p += p->n - 1; y += v->l; z += v->c[a];
+			for (; y >= x; --p) y -= p->l, z -= p->c[a];
+			++p;
+		} else for (; y + p->l < x; ++p) y += p->l, z += p->c[a]; // then search forwardly
+		assert(p - u < u->n);
+		if (v) v->c[a] += rl, v->l += rl; // we should not change p->c[a] because this may cause troubles when p's child is split
+		v = p; p = p->p; // descend
+	} while (!u->is_bottom);
+	rope->c[a] += rl; // $rope->c should be updated after the loop as adding a new root needs the old $rope->c counts
+	if (cache) {
+		if (cache->p != (uint8_t*)p) memset(cache, 0, sizeof(rpcache_t));
+		n_runs = rle_insert_cached((uint8_t*)p, x - y, a, rl, cnt, v->c, &cache->beg, cache->bc);
+		cache->p = (uint8_t*)p;
+	} else n_runs = rle_insert((uint8_t*)p, x - y, a, rl, cnt, v->c);
+	z += cnt[a];
+	v->c[a] += rl; v->l += rl; // this should be after rle_insert(); otherwise rle_insert() won't work
+	if (n_runs + RLE_MIN_SPACE > rope->block_len) {
+		split_node(rope, u, v);
+		if (cache) memset(cache, 0, sizeof(rpcache_t));
+	}
+	return z;
+}
+
+static rpnode_t *rope_count_to_leaf(const rope_t *rope, int64_t x, int64_t cx[6], int64_t *rest)
+{
+	rpnode_t *u, *v = 0, *p = rope->root;
+	int64_t y = 0;
+	int a;
+
+	memset(cx, 0, 48);
+	do {
+		u = p;
+		if (v && x - y > v->l>>1) {
+			p += p->n - 1; y += v->l;
+			for (a = 0; a != 6; ++a) cx[a] += v->c[a];
+			for (; y >= x; --p) {
+				y -= p->l;
+				for (a = 0; a != 6; ++a) cx[a] -= p->c[a];
+			}
+			++p;
+		} else {
+			for (; y + p->l < x; ++p) {
+				y += p->l;
+				for (a = 0; a != 6; ++a) cx[a] += p->c[a];
+			}
+		}
+		v = p; p = p->p;
+	} while (!u->is_bottom);
+	*rest = x - y;
+	return v;
+}
+
+void rope_rank2a(const rope_t *rope, int64_t x, int64_t y, int64_t *cx, int64_t *cy)
+{
+	rpnode_t *v;
+	int64_t rest;
+	v = rope_count_to_leaf(rope, x, cx, &rest);
+	if (y < x || cy == 0) {
+		rle_rank1a((const uint8_t*)v->p, rest, cx, v->c);
+	} else if (rest + (y - x) <= v->l) {
+		memcpy(cy, cx, 48);
+		rle_rank2a((const uint8_t*)v->p, rest, rest + (y - x), cx, cy, v->c);
+	} else {
+		rle_rank1a((const uint8_t*)v->p, rest, cx, v->c);
+		v = rope_count_to_leaf(rope, y, cy, &rest);
+		rle_rank1a((const uint8_t*)v->p, rest, cy, v->c);
+	}
+}
+
+/*********************
+ *** Rope iterator ***
+ *********************/
+
+void rope_itr_first(const rope_t *rope, rpitr_t *i)
+{
+	memset(i, 0, sizeof(rpitr_t));
+	i->rope = rope;
+	for (i->pa[i->d] = rope->root; !i->pa[i->d]->is_bottom;) // descend to the leftmost leaf
+		++i->d, i->pa[i->d] = i->pa[i->d - 1]->p;
+}
+
+const uint8_t *rope_itr_next_block(rpitr_t *i)
+{
+	const uint8_t *ret;
+	assert(i->d < ROPE_MAX_DEPTH); // a B+ tree should not be that tall
+	if (i->d < 0) return 0;
+	ret = (uint8_t*)i->pa[i->d][i->ia[i->d]].p;
+	while (i->d >= 0 && ++i->ia[i->d] == i->pa[i->d]->n) i->ia[i->d--] = 0; // backtracking
+	if (i->d >= 0)
+		while (!i->pa[i->d]->is_bottom) // descend to the leftmost leaf
+			++i->d, i->pa[i->d] = i->pa[i->d - 1][i->ia[i->d - 1]].p;
+	return ret;
+}
+
+/***********
+ *** I/O ***
+ ***********/
+
+void rope_print_node(const rpnode_t *p)
+{
+	if (p->is_bottom) {
+		int i;
+		putchar('(');
+		for (i = 0; i < p->n; ++i) {
+			uint8_t *block = (uint8_t*)p[i].p;
+			const uint8_t *q = block + 2, *end = block + 2 + *rle_nptr(block);
+			if (i) putchar(',');
+			while (q < end) {
+				int c = 0;
+				int64_t j, l;
+				rle_dec1(q, c, l);
+				for (j = 0; j < l; ++j) putchar("$ACGTN"[c]);
+			}
+		}
+		putchar(')');
+	} else {
+		int i;
+		putchar('(');
+		for (i = 0; i < p->n; ++i) {
+			if (i) putchar(',');
+			rope_print_node(p[i].p);
+		}
+		putchar(')');
+	}
+}
+
+void rope_dump_node(const rpnode_t *p, FILE *fp)
+{
+	int16_t i, n = p->n;
+	uint8_t is_bottom = p->is_bottom;
+	fwrite(&is_bottom, 1, 1, fp);
+	fwrite(&n, 2, 1, fp);
+	if (is_bottom) {
+		for (i = 0; i < n; ++i) {
+			fwrite(p[i].c, 8, 6, fp);
+			fwrite(p[i].p, 1, *rle_nptr(p[i].p) + 2, fp);
+		}
+	} else {
+		for (i = 0; i < p->n; ++i)
+			rope_dump_node(p[i].p, fp);
+	}
+}
+
+void rope_dump(const rope_t *r, FILE *fp)
+{
+	fwrite(&r->max_nodes, 4, 1, fp);
+	fwrite(&r->block_len, 4, 1, fp);
+	rope_dump_node(r->root, fp);
+}
+
+rpnode_t *rope_restore_node(const rope_t *r, FILE *fp, int64_t c[6])
+{
+	uint8_t is_bottom, a;
+	int16_t i, n;
+	rpnode_t *p;
+	fread(&is_bottom, 1, 1, fp);
+	fread(&n, 2, 1, fp);
+	p = mp_alloc(r->node);
+	p->is_bottom = is_bottom, p->n = n;
+	if (is_bottom) {
+		for (i = 0; i < n; ++i) {
+			uint16_t *q;
+			p[i].p = mp_alloc(r->leaf);
+			q = rle_nptr(p[i].p);
+			fread(p[i].c, 8, 6, fp);
+			fread(q, 2, 1, fp);
+			fread(q + 1, 1, *q, fp);
+		}
+	} else {
+		for (i = 0; i < n; ++i)
+			p[i].p = rope_restore_node(r, fp, p[i].c);
+	}
+	memset(c, 0, 48);
+	for (i = 0; i < n; ++i) {
+		p[i].l = 0;
+		for (a = 0; a < 6; ++a)
+			c[a] += p[i].c[a], p[i].l += p[i].c[a];
+	}
+	return p;
+}
+
+rope_t *rope_restore(FILE *fp)
+{
+	rope_t *r;
+	r = calloc(1, sizeof(rope_t));
+	fread(&r->max_nodes, 4, 1, fp);
+	fread(&r->block_len, 4, 1, fp);
+	r->node = mp_init(sizeof(rpnode_t) * r->max_nodes);
+	r->leaf = mp_init(r->block_len);
+	r->root = rope_restore_node(r, fp, r->c);
+	return r;
+}

rope.h

@@ -0,0 +1,58 @@
+#ifndef ROPE_H_
+#define ROPE_H_
+
+#include <stdint.h>
+#include <stdio.h>
+
+#define ROPE_MAX_DEPTH 80
+#define ROPE_DEF_MAX_NODES 64
+#define ROPE_DEF_BLOCK_LEN 512
+
+typedef struct rpnode_s {
+	struct rpnode_s *p; // child; at the bottom level, $p points to a string with the first 2 bytes giving the number of runs (#runs)
+	uint64_t l:54, n:9, is_bottom:1; // $n and $is_bottom are only set for the first node in a bucket
+	int64_t c[6]; // marginal counts
+} rpnode_t;
+
+typedef struct {
+	int32_t max_nodes, block_len; // both MUST BE even numbers
+	int64_t c[6]; // marginal counts
+	rpnode_t *root;
+	void *node, *leaf; // memory pool
+} rope_t;
+
+typedef struct {
+	const rope_t *rope; // the rope
+	const rpnode_t *pa[ROPE_MAX_DEPTH]; // parent nodes
+	int ia[ROPE_MAX_DEPTH]; // index in the parent nodes
+	int d; // the current depth in the B+-tree
+} rpitr_t;
+
+typedef struct {
+	int beg;
+	int64_t bc[6];
+	uint8_t *p;
+} rpcache_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	rope_t *rope_init(int max_nodes, int block_len);
+	void rope_destroy(rope_t *rope);
+	int64_t rope_insert_run(rope_t *rope, int64_t x, int a, int64_t rl, rpcache_t *cache);
+	void rope_rank2a(const rope_t *rope, int64_t x, int64_t y, int64_t *cx, int64_t *cy);
+	#define rope_rank1a(rope, x, cx) rope_rank2a(rope, x, -1, cx, 0)
+
+	void rope_itr_first(const rope_t *rope, rpitr_t *i);
+	const uint8_t *rope_itr_next_block(rpitr_t *i);
+
+	void rope_print_node(const rpnode_t *p);
+	void rope_dump(const rope_t *r, FILE *fp);
+	rope_t *rope_restore(FILE *fp);
+	
+#ifdef __cplusplus
+}
+#endif
+
+#endif

scalar_sse.h

@@ -0,0 +1,119 @@
+#ifndef SCALAR_SSE_H
+#define SCALAR_SSE_H
+
+#include <assert.h>
+#include <stdint.h>
+#include <string.h>
+
+typedef union m128i {
+	uint8_t u8[16];
+	int16_t i16[8];
+} __m128i;
+
+static inline __m128i _mm_set1_epi32(int32_t n) {
+	assert(n >= 0 && n <= 255);
+	__m128i r; memset(&r, n, sizeof r); return r;
+}
+
+static inline __m128i _mm_load_si128(const __m128i *ptr) { __m128i r; memcpy(&r, ptr, sizeof r); return r; }
+static inline void _mm_store_si128(__m128i *ptr, __m128i a) { memcpy(ptr, &a, sizeof a); }
+
+static inline int m128i_allzero(__m128i a) {
+	static const char zero[] = "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
+	return memcmp(&a, zero, sizeof a) == 0;
+}
+
+static inline __m128i _mm_slli_si128(__m128i a, int n) {
+	int i;
+	memmove(&a.u8[n], &a.u8[0], 16 - n);
+	for (i = 0; i < n; i++) a.u8[i] = 0;
+	return a;
+}
+
+static inline __m128i _mm_adds_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++) {
+		uint16_t aa = a.u8[i];
+		aa += b.u8[i];
+		a.u8[i] = (aa < 256)? aa : 255;
+	}
+	return a;
+}
+
+static inline __m128i _mm_max_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++)
+		if (a.u8[i] < b.u8[i]) a.u8[i] = b.u8[i];
+	return a;
+}
+
+static inline uint8_t m128i_max_u8(__m128i a) {
+	uint8_t max = 0;
+	int i;
+	for (i = 0; i < 16; i++)
+		if (max < a.u8[i]) max = a.u8[i];
+	return max;
+}
+
+static inline __m128i _mm_set1_epi8(int8_t n) { __m128i r; memset(&r, n, sizeof r); return r; }
+
+static inline __m128i _mm_subs_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++) {
+		int16_t aa = a.u8[i];
+		aa -= b.u8[i];
+		a.u8[i] = (aa >= 0)? aa : 0;
+	}
+	return a;
+}
+
+static inline __m128i _mm_adds_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++) {
+		int32_t aa = a.i16[i];
+		aa += b.i16[i];
+		a.i16[i] = (aa < 32768)? aa : 32767;
+	}
+	return a;
+}
+
+static inline __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++)
+		a.i16[i] = (a.i16[i] > b.i16[i])? 0xffff : 0x0000;
+	return a;
+}
+
+static inline __m128i _mm_max_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++)
+		if (a.i16[i] < b.i16[i]) a.i16[i] = b.i16[i];
+	return a;
+}
+
+static inline __m128i _mm_set1_epi16(int16_t n) {
+	__m128i r;
+	r.i16[0] = r.i16[1] = r.i16[2] = r.i16[3] =
+	r.i16[4] = r.i16[5] = r.i16[6] = r.i16[7] = n;
+	return r;
+}
+
+static inline int16_t m128i_max_s16(__m128i a) {
+	int16_t max = -32768;
+	int i;
+	for (i = 0; i < 8; i++)
+		if (max < a.i16[i]) max = a.i16[i];
+	return max;
+}
+
+static inline __m128i _mm_subs_epu16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++) {
+		int32_t aa = a.i16[i];
+		aa -= b.i16[i];
+		a.i16[i] = (aa >= 0)? aa : 0;
+	}
+	return a;
+}
+
+#endif

utils.c

@@ -0,0 +1,306 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#define FSYNC_ON_FLUSH
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <errno.h>
+#ifdef FSYNC_ON_FLUSH
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#endif
+#include <sys/resource.h>
+#include <sys/time.h>
+#include "utils.h"
+
+#include "ksort.h"
+#define pair64_lt(a, b) ((a).x < (b).x || ((a).x == (b).x && (a).y < (b).y))
+KSORT_INIT(128, pair64_t, pair64_lt)
+KSORT_INIT(64,  uint64_t, ks_lt_generic)
+
+#include "kseq.h"
+KSEQ_INIT2(, gzFile, err_gzread)
+
+/********************
+ * System utilities *
+ ********************/
+
+FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
+{
+	FILE *fp = 0;
+	if (strcmp(fn, "-") == 0)
+		return (strstr(mode, "r"))? stdin : stdout;
+	if ((fp = fopen(fn, mode)) == 0) {
+		err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
+	}
+	return fp;
+}
+
+FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
+{
+	if (freopen(fn, mode, fp) == 0) {
+		err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
+	}
+	return fp;
+}
+
+gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
+{
+	gzFile fp;
+	if (strcmp(fn, "-") == 0) {
+		fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+		/* According to zlib.h, this is the only reason gzdopen can fail */
+		if (!fp) err_fatal(func, "Out of memory");
+		return fp;
+	}
+	if ((fp = gzopen(fn, mode)) == 0) {
+		err_fatal(func, "fail to open file '%s' : %s", fn, errno ? strerror(errno) : "Out of memory");
+	}
+	return fp;
+}
+
+void err_fatal(const char *header, const char *fmt, ...)
+{
+	va_list args;
+	va_start(args, fmt);
+	fprintf(stderr, "[%s] ", header);
+	vfprintf(stderr, fmt, args);
+	fprintf(stderr, "\n");
+	va_end(args);
+	exit(EXIT_FAILURE);
+}
+
+void err_fatal_core(const char *header, const char *fmt, ...)
+{
+	va_list args;
+	va_start(args, fmt);
+	fprintf(stderr, "[%s] ", header);
+	vfprintf(stderr, fmt, args);
+	fprintf(stderr, " Abort!\n");
+	va_end(args);
+	abort();
+}
+
+void _err_fatal_simple(const char *func, const char *msg)
+{
+	fprintf(stderr, "[%s] %s\n", func, msg);
+	exit(EXIT_FAILURE);
+}
+
+void _err_fatal_simple_core(const char *func, const char *msg)
+{
+	fprintf(stderr, "[%s] %s Abort!\n", func, msg);
+	abort();
+}
+
+size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
+{
+	size_t ret = fwrite(ptr, size, nmemb, stream);
+	if (ret != nmemb) 
+		_err_fatal_simple("fwrite", strerror(errno));
+	return ret;
+}
+
+size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream)
+{
+	size_t ret = fread(ptr, size, nmemb, stream);
+	if (ret != nmemb)
+	{
+		_err_fatal_simple("fread", ferror(stream) ? strerror(errno) : "Unexpected end of file");
+	}
+	return ret;
+}
+
+int err_gzread(gzFile file, void *ptr, unsigned int len)
+{
+	int ret = gzread(file, ptr, len);
+
+	if (ret < 0)
+	{
+		int errnum = 0;
+		const char *msg = gzerror(file, &errnum);
+		_err_fatal_simple("gzread", Z_ERRNO == errnum ? strerror(errno) : msg);
+	}
+
+	return ret;
+}
+
+int err_fseek(FILE *stream, long offset, int whence)
+{
+	int ret = fseek(stream, offset, whence);
+	if (0 != ret)
+	{
+		_err_fatal_simple("fseek", strerror(errno));
+	}
+	return ret;
+}
+
+long err_ftell(FILE *stream)
+{
+	long ret = ftell(stream);
+	if (-1 == ret)
+	{
+		_err_fatal_simple("ftell", strerror(errno));
+	}
+	return ret;
+}
+
+int err_printf(const char *format, ...) 
+{
+	va_list arg;
+	int done;
+	va_start(arg, format);
+	done = vfprintf(stdout, format, arg);
+	int saveErrno = errno;
+	va_end(arg);
+	if (done < 0) _err_fatal_simple("vfprintf(stdout)", strerror(saveErrno));
+	return done;
+}
+
+int err_fprintf(FILE *stream, const char *format, ...) 
+{
+	va_list arg;
+	int done;
+	va_start(arg, format);
+	done = vfprintf(stream, format, arg);
+	int saveErrno = errno;
+	va_end(arg);
+	if (done < 0) _err_fatal_simple("vfprintf", strerror(saveErrno));
+	return done;
+}
+
+int err_fputc(int c, FILE *stream)
+{
+	int ret = putc(c, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputc", strerror(errno));
+	}
+
+	return ret;
+}
+
+int err_fputs(const char *s, FILE *stream)
+{
+	int ret = fputs(s, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputs", strerror(errno));
+	}
+
+	return ret;
+}
+
+int err_puts(const char *s)
+{
+	int ret = puts(s);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("puts", strerror(errno));
+	}
+
+	return ret;
+}
+
+int err_fflush(FILE *stream) 
+{
+    int ret = fflush(stream);
+    if (ret != 0) _err_fatal_simple("fflush", strerror(errno));
+
+#ifdef FSYNC_ON_FLUSH
+	/* Calling fflush() ensures that all the data has made it to the
+	   kernel buffers, but this may not be sufficient for remote filesystems
+	   (e.g. NFS, lustre) as an error may still occur while the kernel
+	   is copying the buffered data to the file server.  To be sure of
+	   catching these errors, we need to call fsync() on the file
+	   descriptor, but only if it is a regular file.  */
+	{
+		struct stat sbuf;
+		if (0 != fstat(fileno(stream), &sbuf))
+			_err_fatal_simple("fstat", strerror(errno));
+		
+		if (S_ISREG(sbuf.st_mode))
+		{
+			if (0 != fsync(fileno(stream)))
+				_err_fatal_simple("fsync", strerror(errno));
+		}
+	}
+#endif
+    return ret;
+}
+
+int err_fclose(FILE *stream) 
+{
+	int ret = fclose(stream);
+	if (ret != 0) _err_fatal_simple("fclose", strerror(errno));
+	return ret;
+}
+
+int err_gzclose(gzFile file)
+{
+	int ret = gzclose(file);
+	if (Z_OK != ret)
+	{
+		_err_fatal_simple("gzclose", Z_ERRNO == ret ? strerror(errno) : zError(ret));
+	}
+
+	return ret;
+}
+
+/*********
+ * Timer *
+ *********/
+
+double cputime(void)
+{
+	struct rusage r;
+	getrusage(RUSAGE_SELF, &r);
+	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
+}
+
+double realtime(void)
+{
+	struct timeval tp;
+	struct timezone tzp;
+	gettimeofday(&tp, &tzp);
+	return tp.tv_sec + tp.tv_usec * 1e-6;
+}
+
+long peakrss(void)
+{
+	struct rusage r;
+	getrusage(RUSAGE_SELF, &r);
+#ifdef __linux__
+	return r.ru_maxrss * 1024;
+#else
+	return r.ru_maxrss;
+#endif
+}

utils.h

@@ -0,0 +1,111 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+#ifndef LH3_UTILS_H
+#define LH3_UTILS_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#ifdef __GNUC__
+// Tell GCC to validate printf format string and args
+#define ATTRIBUTE(list) __attribute__ (list)
+#else
+#define ATTRIBUTE(list)
+#endif
+
+#define err_fatal_simple(msg) _err_fatal_simple(__func__, msg)
+#define err_fatal_simple_core(msg) _err_fatal_simple_core(__func__, msg)
+
+#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
+#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
+#define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)
+
+#define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg)
+
+typedef struct {
+	uint64_t x, y;
+} pair64_t;
+
+typedef struct { size_t n, m; uint64_t *a; } uint64_v;
+typedef struct { size_t n, m; pair64_t *a; } pair64_v;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void err_fatal(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
+	void err_fatal_core(const char *header, const char *fmt, ...) ATTRIBUTE((noreturn));
+	void _err_fatal_simple(const char *func, const char *msg) ATTRIBUTE((noreturn));
+	void _err_fatal_simple_core(const char *func, const char *msg) ATTRIBUTE((noreturn));
+	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
+	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
+	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
+    size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
+	size_t err_fread_noeof(void *ptr, size_t size, size_t nmemb, FILE *stream);
+
+	int err_gzread(gzFile file, void *ptr, unsigned int len);
+	int err_fseek(FILE *stream, long offset, int whence);
+#define err_rewind(FP) err_fseek((FP), 0, SEEK_SET)
+	long err_ftell(FILE *stream);
+	int err_fprintf(FILE *stream, const char *format, ...)
+        ATTRIBUTE((format(printf, 2, 3)));
+	int err_printf(const char *format, ...)
+        ATTRIBUTE((format(printf, 1, 2)));
+	int err_fputc(int c, FILE *stream);
+#define err_putchar(C) err_fputc((C), stdout)
+	int err_fputs(const char *s, FILE *stream);
+	int err_puts(const char *s);
+	int err_fflush(FILE *stream);
+	int err_fclose(FILE *stream);
+	int err_gzclose(gzFile file);
+
+	double cputime(void);
+	double realtime(void);
+	long peakrss(void);
+
+	void ks_introsort_64 (size_t n, uint64_t *a);
+	void ks_introsort_128(size_t n, pair64_t *a);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline uint64_t hash_64(uint64_t key)
+{
+	key += ~(key << 32);
+	key ^= (key >> 22);
+	key += ~(key << 13);
+	key ^= (key >> 8);
+	key += (key << 3);
+	key ^= (key >> 15);
+	key += ~(key << 27);
+	key ^= (key >> 31);
+	return key;
+}
+
+#endif

xa2multi.pl

@@ -0,0 +1,25 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+while (<>) {
+	if (/\tXA:Z:(\S+)/) {
+		my $l = $1;
+		print;
+		my @t = split("\t");
+		while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
+			my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
+			my $seq = $t[9];
+			my $phred = $t[10];
+			# if alternative alignment has other orientation than primary, 
+			# then print the reverse (complement) of sequence and phred string
+			if ((($t[1]&0x10)>0) xor ($2<0)) {
+				$seq = reverse $seq;
+				$seq =~ tr/ACGTacgt/TGCAtgca/;
+				$phred = reverse $phred;
+			}
+			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
+		}
+	} else { print; }
+}