API: aln seems working

Makefile

@@ -2,16 +2,19 @@ CC=			gcc
 CXX=		g++
 CFLAGS=		-g -Wall -O2
 CXXFLAGS=	$(CFLAGS)
+AR=			ar
 DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
-OBJS=		QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
-			is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o \
-			bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
+LOBJS=		bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \
+			bwaseqio.o
+AOBJS=		QSufSort.o bwt_gen.o \
+			is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
+			bwase.o bwape.o kstring.o cs2nt.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
-			bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o
+			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa
 INCLUDES=	
 LIBS=		-lm -lz -lpthread
-SUBDIRS=	. bwt_gen
+SUBDIRS=	.
 
 .SUFFIXES:.c .o .cc
 
@@ -22,19 +25,21 @@ SUBDIRS=	. bwt_gen
 
 all:$(PROG)
 
-bwa:$(OBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
+bwa:libbwa.a $(AOBJS) main.o
+		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+libbwa.a:$(LOBJS)
+		$(AR) -csru $@ $(LOBJS)
+
+bwa.o:bwa.h
 
 QSufSort.o:QSufSort.h
 
 bwt.o:bwt.h
 bwtio.o:bwt.h
 bwtaln.o:bwt.h bwtaln.h kseq.h
-bwt1away.o:bwt.h bwtaln.h
-bwt2fmv.o:bwt.h
 bntseq.o:bntseq.h
 bwtgap.o:bwtgap.h bwtaln.h bwt.h
-fastmap:bwt.h
 
 bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h

bwa.c

@@ -0,0 +1,126 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include "bwa.h"
+#include "bwt.h"
+#include "bwtgap.h"
+#include "bntseq.h"
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+extern unsigned char nst_nt4_table[256];
+
+bwa_opt_t bwa_def_opt = { 11, 4, -1, 1, 6, 32, 2, 0.04 };
+
+struct bwa_idx_t {
+	bwt_t *bwt;
+	bntseq_t *bns;
+	uint8_t *pac;
+};
+
+struct bwa_aux_t {
+	int max_buf;
+	gap_stack_t *stack;
+	gap_opt_t *opt;
+	int *diff_tab;
+	uint8_t *buf;
+};
+
+bwa_idx_t *bwa_idx_load(const char *prefix)
+{
+	bwa_idx_t *p;
+	int l;
+	char *str;
+	l = strlen(prefix);
+	p = calloc(1, sizeof(bwa_idx_t));
+	str = malloc(l + 10);
+	strcpy(str, prefix);
+	p->bns = bns_restore(str);
+	strcpy(str + l, ".bwt");
+	p->bwt = bwt_restore_bwt(str);
+	str[l] = 0;
+	strcpy(str + l, ".sa");
+	bwt_restore_sa(str, p->bwt);
+	free(str);
+	p->pac = calloc(p->bns->l_pac/4+1, 1);
+	fread(p->pac, 1, p->bns->l_pac/4+1, p->bns->fp_pac);
+	fclose(p->bns->fp_pac);
+	p->bns->fp_pac = 0;
+	return p;
+}
+
+void bwa_idx_destroy(bwa_idx_t *p)
+{
+	bns_destroy(p->bns);
+	bwt_destroy(p->bwt);
+	free(p->pac);
+	free(p);
+}
+
+bwa_aux_t *bwa_aux_init(const bwa_opt_t *opt, int max_score)
+{
+	extern gap_opt_t *gap_init_opt(void);
+	extern int bwa_cal_maxdiff(int l, double err, double thres);
+	int i;
+	bwa_aux_t *p;
+	p = malloc(sizeof(bwa_aux_t));
+	p->stack = gap_init_stack2(max_score);
+	p->opt = gap_init_opt();
+	p->opt->s_gapo = opt->s_gapo;
+	p->opt->s_gape = opt->s_gape;
+	p->opt->max_diff = opt->max_diff;
+	p->opt->max_gapo = opt->max_gapo;
+	p->opt->max_gape = opt->max_gape;
+	p->opt->seed_len = opt->seed_len;
+	p->opt->max_seed_diff = opt->max_seed_diff;
+	p->opt->fnr = opt->fnr;
+	p->diff_tab = calloc(BWA_MAX_QUERY_LEN, sizeof(int));
+	for (i = 1; i < BWA_MAX_QUERY_LEN; ++i)
+		p->diff_tab[i] = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
+	return p;
+}
+
+void bwa_aux_destroy(bwa_aux_t *p)
+{
+	gap_destroy_stack(p->stack);
+	free(p->diff_tab); free(p->opt);
+	free(p);
+}
+
+bwa_alnpre_t *bwa_aln_pre(const bwa_idx_t *idx, bwa_aux_t *aux, const char *seq, int *n_aln)
+{
+	extern int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width);
+	extern void seq_reverse(int len, uint8_t *seq, int is_comp);
+	int i, seq_len, buf_len;
+	bwt_width_t *w, *seed_w;
+	uint8_t *s;
+	gap_opt_t opt2 = *aux->opt;
+
+	seq_len = strlen(seq);
+	// estimate the buffer length
+	buf_len = (aux->opt->seed_len + seq_len + 1) * sizeof(bwt_width_t) + seq_len;
+	if (buf_len > aux->max_buf) {
+		aux->max_buf = buf_len;
+		kroundup32(aux->max_buf);
+		aux->buf = realloc(aux->buf, aux->max_buf);
+	}
+	memset(aux->buf, 0, buf_len);
+	seed_w = (bwt_width_t*)aux->buf;
+	w = seed_w + aux->opt->seed_len;
+	s = (uint8_t*)(w + seq_len + 1);
+	if (opt2.fnr > 0.) opt2.max_diff = aux->diff_tab[seq_len];
+	// copy the sequence
+	for (i = 0; i < seq_len; ++i)
+		s[i] = nst_nt4_table[(int)seq[i]];
+	seq_reverse(seq_len, s, 0);
+	// mapping
+	bwt_cal_width(idx->bwt, seq_len, s, w);
+	if (opt2.seed_len >= seq_len) opt2.seed_len = 0x7fffffff;
+	if (seq_len > aux->opt->seed_len)
+		bwt_cal_width(idx->bwt, aux->opt->seed_len, s + (seq_len - aux->opt->seed_len), seed_w);
+	for (i = 0; i < seq_len; ++i) // complement; I forgot why...
+		s[i] = s[i] > 3? 4 : 3 - s[i];
+	return (bwa_alnpre_t*)bwt_match_gap(idx->bwt, seq_len, s, w, seq_len <= aux->opt->seed_len? 0 : seed_w, &opt2, n_aln, aux->stack);
+}

bwa.h

@@ -0,0 +1,44 @@
+#ifndef BWA_H_
+#define BWA_H_
+
+#include <stdint.h>
+
+#define BWA_DEF_MAX_SCORE 2048
+#define BWA_MAX_QUERY_LEN 1024
+
+struct bwa_idx_t;
+typedef struct bwa_idx_t bwa_idx_t;
+
+struct bwa_aux_t;
+typedef struct bwa_aux_t bwa_aux_t;
+
+typedef struct {
+	int s_gapo, s_gape; // the mismatch penalty is fixed at 3
+	int max_diff, max_gapo, max_gape;
+	int seed_len, max_seed_diff;
+	float fnr;
+} bwa_opt_t;
+
+typedef struct {
+	uint32_t n_mm:16, n_gapo:8, n_gape:8;
+	int score;
+	uint64_t k, l;
+} bwa_alnpre_t;
+
+extern bwa_opt_t bwa_def_opt;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bwa_idx_t *bwa_idx_load(const char *prefix);
+	void bwa_idx_destroy(bwa_idx_t *p);
+	bwa_aux_t *bwa_aux_init(const bwa_opt_t *opt, int max_score);
+	void bwa_aux_destroy(bwa_aux_t *p);
+	bwa_alnpre_t *bwa_aln_pre(const bwa_idx_t *idx, bwa_aux_t *aux, const char *seq, int *n_aln);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

bwtaln.c

@@ -49,7 +49,7 @@ int bwa_cal_maxdiff(int l, double err, double thres)
 }
 
 // width must be filled as zero
-static int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width)
+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;

bwtgap.c

@@ -10,21 +10,20 @@
 
 #define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)
 
-gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
+gap_stack_t *gap_init_stack2(int max_score)
 {
-	int i;
 	gap_stack_t *stack;
 	stack = (gap_stack_t*)calloc(1, sizeof(gap_stack_t));
-	stack->n_stacks = aln_score(max_mm+1, max_gapo+1, max_gape+1, opt);
+	stack->n_stacks = max_score;
 	stack->stacks = (gap_stack1_t*)calloc(stack->n_stacks, sizeof(gap_stack1_t));
-	for (i = 0; i != stack->n_stacks; ++i) {
-		gap_stack1_t *p = stack->stacks + i;
-		p->m_entries = 4;
-		p->stack = (gap_entry_t*)calloc(p->m_entries, sizeof(gap_entry_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;
@@ -51,7 +50,7 @@ static inline void gap_push(gap_stack_t *stack, int i, bwtint_t k, bwtint_t l, i
 	score = aln_score(n_mm, n_gapo, n_gape, opt);
 	q = stack->stacks + score;
 	if (q->n_entries == q->m_entries) {
-		q->m_entries <<= 1;
+		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;

bwtgap.h

@@ -25,6 +25,7 @@ typedef struct {
 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,