添加了一些注释

.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
+            }
+        }
+    ]
+}

Makefile

@@ -1,6 +1,7 @@
 CC=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+# 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)

bntseq.c

@@ -231,39 +231,39 @@ void bns_destroy(bntseq_t *bns)
 
 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;
+	bntann1_t *p; // 染色体，contig
 	int i, lasts;
-	if (bns->n_seqs == *m_seqs) {
+	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->name = strdup((char*)seq->name.s);
-	p->anno = seq->comment.l > 0? strdup((char*)seq->comment.s) : strdup("(null)");
-	p->gi = 0; p->len = seq->seq.l;
-	p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
-	p->n_ambs = 0;
-	for (i = lasts = 0; i < seq->seq.l; ++i) {
-		int c = nst_nt4_table[(int)seq->seq.s[i]];
+	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;
-			} else {
-				if (bns->n_holes == *m_holes) {
+				++(*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;
+				(*q)->offset = p->offset + i; // 模棱两可碱基偏移
 				(*q)->amb = seq->seq.s[i];
-				++p->n_ambs;
-				++bns->n_holes;
+				++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];
+		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;
+			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);

bntseq.h

@@ -57,9 +57,9 @@ typedef struct {
 	int64_t l_pac;
 	int32_t n_seqs;
 	uint32_t seed;
-	bntann1_t *anns; // n_seqs elements
+	bntann1_t *anns; // n_seqs elements 染色体
 	int32_t n_holes;
-	bntamb1_t *ambs; // n_holes elements
+	bntamb1_t *ambs; // n_holes elements 非AGCT字符
 	FILE *fp_pac;
 } bntseq_t;
 

bwt.c

@@ -39,6 +39,7 @@
 #  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;
@@ -52,17 +53,23 @@ void bwt_gen_cnt_table(bwt_t *bwt)
 
 static inline bwtint_t bwt_invPsi(const bwt_t *bwt, bwtint_t k) // compute inverse CSA
 {
-	bwtint_t x = k - (k > bwt->primary);
-	x = bwt_B0(bwt, x);
-	x = bwt->L2[x] + bwt_occ(bwt, k, x);
+	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
-	int intv_round = 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.");
@@ -71,13 +78,13 @@ void bwt_cal_sa(bwt_t *bwt, int intv)
 	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));
+	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;
-		--sa;
-		isa = bwt_invPsi(bwt, isa);
+		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
@@ -286,6 +293,7 @@ static void bwt_reverse_intvs(bwtintv_v *p)
 	}
 }
 // 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;