r334: added pemerge to bwa

Makefile

@@ -5,7 +5,7 @@ AR=			ar
 DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
 LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
 AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-			is.o bwtindex.o bwape.o kopen.o \
+			is.o bwtindex.o bwape.o kopen.o pemerge.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa bwamem-lite

bntseq.c

@@ -31,7 +31,6 @@
 #include <zlib.h>
 #include <unistd.h>
 #include "bntseq.h"
-#include "main.h"
 #include "utils.h"
 
 #include "kseq.h"

main.c

@@ -1,12 +1,29 @@
 #include <stdio.h>
 #include <string.h>
-#include "main.h"
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r332-beta"
+#define PACKAGE_VERSION "0.7.0-r334-beta"
 #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_pemerge(int argc, char *argv[]);
+
 static int usage()
 {
 	fprintf(stderr, "\n");
@@ -15,12 +32,13 @@ static int usage()
 	fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\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\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\n");
-	fprintf(stderr, "         fastmap       identify super-maximal exact matches\n");
-	fprintf(stderr, "         mem           BWA-MEM algorithm\n");
 	fprintf(stderr, "\n");
 	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
 	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
@@ -56,6 +74,7 @@ int main(int argc, char *argv[])
 	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], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
 	else {
 		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
 		return 1;

main.h

@@ -1,28 +0,0 @@
-#ifndef BWA_MAIN_H
-#define BWA_MAIN_H
-
-#ifdef __cplusplus
-extern "C" {
-#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 bwa_aln(int argc, char *argv[]);
-	int bwt_bwtgen_main(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[]);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif

pemerge.c

@@ -5,35 +5,8 @@
 #include <zlib.h>
 #include "ksw.h"
 #include "kseq.h"
-
-#ifdef _PEM_MAIN
-KSEQ_INIT(gzFile, gzread)
-
-unsigned char nst_nt4_table[128] = {
-	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
-	4, 4, 4, 4,  4, 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
-};
-
-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++] = 0; // ambiguous base
-	}
-	for (j = 0; j < 5; ++j) mat[k++] = 0;
-}
-#else
 #include "bwa.h"
 KSEQ_DECLARE(gzFile)
-#endif
 
 #define MAX_SCORE_RATIO 0.9f
 #define MAX_ERR 8
@@ -183,11 +156,7 @@ static inline void print_seq(const char *n, const char *s, const char *q)
 	}
 }
 
-#ifdef _PEM_MAIN
-int main(int argc, char *argv[])
-#else
 int main_pemerge(int argc, char *argv[])
-#endif
 {
 	int c, flag = 0, i;
 	int64_t cnt[MAX_ERR+1];
@@ -246,7 +215,6 @@ int main_pemerge(int argc, char *argv[])
 		} else {
 			++cnt[-l_seq];
 			if (flag & 2) {
-				printf("*** %d\n", l_seq);
 				print_seq(r[0].n.s, r[0].s.s, r[0].q.l? r[0].q.s : 0);
 				print_seq(r[1].n.s, r[1].s.s, r[1].q.l? r[1].q.s : 0);
 			}