解决了sa的bug，现在结果和原版一模一样

Makefile

@@ -15,7 +15,7 @@ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
 			fmt_idx.o
 PROG=		bwa
 INCLUDES=	
-LIBS=		-lm -lz -lpthread
+LIBS=		-lm -lz -lpthread -ldl
 SUBDIRS=	.
 
 ifeq ($(shell uname -s),Linux)
@@ -32,6 +32,9 @@ all:$(PROG)
 bwa:libbwa.a $(AOBJS) main.o
 		$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
 
+#bwa:libbwa.a $(AOBJS) main.o
+#		$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) ../sbwa/jemalloc/lib/libjemalloc.a main.o -o $@ -L. -lbwa $(LIBS)
+
 bwamem-lite:libbwa.a example.o
 		$(CC) $(CFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
 

bwa.c

@@ -279,14 +279,12 @@ bwt_t *bwa_idx_load_bwt(const char *hint)
 		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
 		return 0;
 	}
-	fprintf(stderr, "zzh-1\n");
 	tmp = calloc(strlen(prefix) + 5, 1);
 	strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
 	bwt = bwt_restore_bwt(tmp);
-	fprintf(stderr, "zzh-1\n");
+	//strcat(strcpy(tmp, prefix), ".33.4.sa");  // partial suffix array (SA)
-	strcat(strcpy(tmp, prefix), ".33.2.sa");  // partial suffix array (SA)
+	strcat(strcpy(tmp, prefix), ".sa");  // partial suffix array (SA)
 	bwt_restore_sa(tmp, bwt);
-	fprintf(stderr, "zzh-after-sa\n");
 	free(tmp); free(prefix);
 	return bwt;
 }
@@ -330,7 +328,7 @@ FMTIndex *bwa_idx_load_fmt(const char *hint)
 	strcpy(sa_fn, hint);
 	sprintf(suffix, ".33.%d.sa", SA_INTV);
 	strcpy(sa_fn + l_hint, suffix); // partial suffix array (SA)
-//	fmt_restore_sa(sa_fn, fmt);
+	fmt_restore_sa(sa_fn, fmt);
 
 	free(fmt_idx_fn);
 	free(kmer_idx_fn);
@@ -353,9 +351,9 @@ bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which)
 	if (which & BWA_IDX_BWT) {
 		idx->fmt = bwa_idx_load_fmt(hint);
 		// 先和bwt共用sa
-		idx->fmt->sa = idx->bwt->sa;
+		//idx->fmt->sa = idx->bwt->sa;
-		idx->fmt->n_sa = idx->bwt->n_sa;
+		//idx->fmt->n_sa = idx->bwt->n_sa;
-		idx->fmt->sa_intv = idx->bwt->sa_intv;
+		//idx->fmt->sa_intv = idx->bwt->sa_intv;
 	}
 	if (which & BWA_IDX_BNS)
 	{

bwamem.c

@@ -138,6 +138,8 @@ static void smem_aux_destroy(smem_aux_t *a)
 	free(a);
 }
 
+#define USE_FMT 1
+
 static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIndex *fmt, int len, const uint8_t *seq, smem_aux_t *a)
 {
 	int i, k, x = 0, old_n;
@@ -155,11 +157,9 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
 	// fprintf(stderr, "\n");
 
 	// first pass: find all SMEMs
-	//fprintf(fp1, "seq: %ld\n", dn++);
+	fprintf(fp1, "seq: %ld\n", dn++);
 	//fprintf(stderr, "seq: %ld\n", dn++);
 	//dn ++;
-
-#define USE_FMT 1
 	// goto third_seed;
 
 	while (x < len) {
@@ -186,7 +186,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
 				int slen = (uint32_t)p->info - (p->info >> 32); // seed length
 				max_seed_len = fmax(max_seed_len, slen);
 				if (slen >= opt->min_seed_len) {
-					//fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
+					fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
 					kv_push(bwtintv_t, a->mem, *p);
 				}
 			}
@@ -220,11 +220,12 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
 #endif
 		for (i = 0; i < a->mem1.n; ++i) {
 			bwtintv_t *p = &a->mem1.a[i];
-			//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
+			//fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
-			//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
+			// fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
+			// fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
 			int slen = (uint32_t)p->info - (p->info >> 32); 
 			if (slen >= opt->min_seed_len) {
-				//fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
+				fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
 				kv_push(bwtintv_t, a->mem, a->mem1.a[i]);
 			}
 		}
@@ -258,7 +259,8 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
 
 					if (m.x[2] > 0) {
 						kv_push(bwtintv_t, a->mem, m);
-						//bwtintv_t *p = &m;
+						bwtintv_t *p = &m;
+						fprintf(fp1, "%ld %ld %d\n", p->x[2], p->info >> 32, (uint32_t)p->info);
 						//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
 					}
 				} else { // for now, we never come to this block which is slower
@@ -434,8 +436,15 @@ mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, const FMTIndex *fm
 #ifdef SHOW_PERF
 			int64_t tmp_time = realtime_msec();
 #endif
-//			s.rbeg = tmp.pos = bwt_sa(bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
+#if USE_FMT
 			s.rbeg = tmp.pos = fmt_sa(fmt, p->x[0] + k);
+			uint64_t tpos = bwt_sa(bwt, p->x[0] + k);
+			if (s.rbeg != tpos) {
+				fprintf(stderr, "diff: %ld, %ld %ld\n", p->x[0] + k, tmp.pos, tpos);
+			}
+#else
+			s.rbeg = tmp.pos = bwt_sa(bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
+#endif
 #ifdef SHOW_PERF
 			tmp_time = realtime_msec() - tmp_time;
 			__sync_fetch_and_add(&time_bwt_sa, tmp_time);
@@ -1087,7 +1096,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		kputsn("\tMD:Z:", 6, str); kputs((char*)(p->cigar + p->n_cigar), str);
 	}
 	if (m && m->n_cigar) { kputsn("\tMC:Z:", 6, str); add_cigar(opt, m, str, which); }
-	if (m) { kputsn("\tMQ:i:", 6, str); kputw(m->mapq, str);}
+//	if (m) { kputsn("\tMQ:i:", 6, str); kputw(m->mapq, str);}
 	if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
 	if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
 	if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }

bwt.c

@@ -77,7 +77,7 @@ void inline bwt_set_sa(uint8_t *sa_arr, bwtint_t k, bwtint_t val)
 	const bwtint_t start_byte_idx = block_idx + (val_idx_in_block << 2);
 	bwtint_t *sa_addr = (bwtint_t *)(sa_arr + start_byte_idx);
 	// *sa_addr &= (1 << val_idx_in_block) - 1; // 如果开辟内存的时候清零了，这一步可以省略，会清除后面的数据，只适合按递增顺序赋值
-	*sa_addr |= val << val_idx_in_block;
+	*sa_addr |= (val & ((1L << 33) - 1)) << val_idx_in_block;
 }
 
 // 获取某一行的排序值（小端模式）
@@ -129,7 +129,8 @@ void bwt_cal_sa(bwt_t *bwt, int intv)
 	}
 	if (isa % intv == 0)
 		bwt_set_sa(bwt->sa, isa / intv, sa);
-	bwt_set_sa(bwt->sa, 0, (bwtint_t)-1); // before this line, bwt->sa[0] = bwt->seq_len
+	// bwt_set_sa(bwt->sa, 0, (bwtint_t)-1); // 赋值成-1也没问题，set_sa那里已经修正了
+	bwt_set_sa(bwt->sa, 0, 8589934591); // before this line, bwt->sa[0] = bwt->seq_len
 }
 
 bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
@@ -139,6 +140,7 @@ bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
 		++sa;
 		k = bwt_invPsi(bwt, k);
 	}
+	return sa + bwt->sa[k / bwt->sa_intv];
 	/* without setting bwt->sa[0] = -1, the following line should be
 	   changed to (sa + bwt->sa[k/bwt->sa_intv]) % (bwt->seq_len + 1) */
 //#ifdef SHOW_PERF
@@ -527,9 +529,15 @@ void bwt_restore_sa(const char *fn, bwt_t *bwt)
 	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 = (uint8_t*)malloc(SA_BYTES(bwt->n_sa));
+	
-	fprintf(stderr, "zzh-read-sa %ld\n", SA_BYTES(bwt->n_sa));
+	//bwt->sa = (uint8_t*)malloc(SA_BYTES(bwt->n_sa));
-	fread_fix(fp, SA_BYTES(bwt->n_sa), bwt->sa);
+	//fprintf(stderr, "zzh-read-sa %ld\n", SA_BYTES(bwt->n_sa));
+	//fread_fix(fp, SA_BYTES(bwt->n_sa), bwt->sa);
+
+	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.h

@@ -56,7 +56,8 @@ typedef struct {
 	// suffix array
 	int sa_intv;
 	bwtint_t n_sa;
-	uint8_t *sa;
+	//uint8_t *sa;
+	bwtint_t *sa;
 } bwt_t;
 
 typedef struct {

fmt_idx.c

@@ -657,7 +657,12 @@ int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv
     do { kv_push(bwtintv_t, *curr, iv); goto backward_search; } while(0)
 
     // 处理kmer对应的匹配信息
-    for (j = 1, curr->n = 0; j < kmer_len; ++j) {
+    if (only_forward)
+        j = kmer_len - 1;
+    else
+        j = 1;
+    for (curr->n = 0; j < kmer_len; ++j)
+    {
         fmt_kmer_get(fmt, &ok1, qbit, j);
         CHECK_INTV_CHANGE(ik, ok1, x + j + 1);
     }
@@ -667,11 +672,15 @@ int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv
 #define PAC_BASE(pac, l) ((pac)[(l) >> 2] >> ((~(l) & 3) << 1) & 3)
 
     // 扩展kmer之后的碱基
+    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1), 0, 2);
+    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1 + ik.x[2]), 0, 2);
     for (i = (int)ik.info; i + 1 < len; i += 2)
     { // forward search
         if (q[i] < 4 && q[i + 1] < 4)
         {
             fmt_extend2(fmt, &ik, &ok1, &ok2, 0, 3 - q[i], 3 - q[i + 1]);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1), 0, 2);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1 + ok2.x[2]), 0, 2);
             CHECK_INTV_CHANGE(ik, ok1, i + 1);
             CHECK_INTV_CHANGE(ik, ok2, i + 2);
             // 在这里进行判断是否只有一个候选了
@@ -806,6 +815,8 @@ backward_search:
     for (j = 0; j < curr->n; ++j)
     {
         bwtintv_t *p = &curr->a[j]; // 前向扩展的种子
+        __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1), 0, 2);
+        __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1 + p->x[2]), 0, 2);
         uint64_t qbit = 0;
         if (!only_forward && p->info - x < HASH_KMER_LEN) {
             qbit = build_backward_kmer(q, p->info - 1, HASH_KMER_LEN, &kmer_len); // 创建反向kmer
@@ -822,6 +833,8 @@ backward_search:
             if (q[i] < 4 && q[i - 1] < 4) // 两个都可以扩展
             {
                 fmt_extend2(fmt, p, &ok1, &ok2, 1, q[i], q[i - 1]);
+                __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[0] - 1), 0, 2);
+                __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[0] - 1 + ok2.x[2]), 0, 2);
                 CHECK_INTV_ADD_MEM(ok1, i + 1, *p, mem);
                 ok1.info = p->info;
                 CHECK_INTV_ADD_MEM(ok2, i, ok1, mem);
@@ -880,6 +893,8 @@ int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, in
 
     fmt_kmer_get(fmt, &ik, qbit, kmer_len-1); // 初始碱基位置
     ik.info = x + kmer_len;
+    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1), 0, 2);
+    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1 + ik.x[2]), 0, 2);
 
 #define COND_SET_RETURN(iv, ov, start_pos, end_pos, max_intv, min_len) \
     if (iv.x[2] < max_intv && end_pos - start_pos >= min_len)          \
@@ -894,6 +909,8 @@ int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, in
         if (q[i] < 4 && q[i + 1] < 4)
         {
             fmt_extend2(fmt, &ik, &ok1, &ok2, 0, 3 - q[i], 3 - q[i + 1]);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1), 0, 2);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1 + ok2.x[2]), 0, 2);
             COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
             COND_SET_RETURN(ok2, *mem, x, i + 1, max_intv, min_len);
             ik = ok2;

run.sh

@@ -4,19 +4,20 @@ thread=1
 #n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
 #n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
 #reference=~/data/reference/human_g1k_v37_decoy.fasta
-n_r1=~/fastq/sn_r1.fq
+#n_r1=~/fastq/sn_r1.fq
-n_r2=~/fastq/sn_r2.fq
+#n_r2=~/fastq/sn_r2.fq
 #n_r1=~/fastq/ssn_r1.fq
 #n_r2=~/fastq/ssn_r2.fq
 #n_r1=~/fastq/tiny_n_r1.fq
 #n_r2=~/fastq/tiny_n_r2.fq
-#n_r1=~/fastq/diff_r1.fq
+n_r1=~/fastq/diff_r1.fq
-#n_r2=~/fastq/diff_r2.fq
+n_r2=~/fastq/diff_r2.fq
 #n_r1=~/fastq/d_r1.fq
 #n_r2=~/fastq/d_r2.fq
 reference=~/reference/human_g1k_v37_decoy.fasta
-#out=./out.sam
+#out=./ssn.sam
-out=/dev/null
+out=./out.sam
+#out=/dev/null
 #time ./bwa mem -t 12 -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/nm1.fq \