bio-bwa 0.2.0

data/ext/bwtaln.h

@@ -0,0 +1,150 @@
+#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
+
+#ifndef bns_pac
+#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
+#endif
+
+typedef struct {
+	bwtint_t w;
+	int bid;
+} bwt_width_t;
+
+typedef struct {
+	uint32_t n_mm:8, n_gapo:8, n_gape:8, a:1;
+	bwtint_t k, l;
+	int score;
+} 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 pos;
+	uint32_t n_cigar:15, gap:8, mm:8, strand:1;
+	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 n_cigar;
+	bwa_cigar_t *cigar;
+	// for multi-threading only
+	int tid;
+	// barcode
+	char bc[16]; // null terminated; up to 15 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_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
+#define BWA_PET_SOLID 2
+
+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[2], 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);
+
+
+	/* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
+	__cigar_op and __cigar_len while keeping stdaln stand alone */
+#include "stdaln.h"
+
+	bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

data/ext/bwtgap.c

@@ -0,0 +1,264 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "bwtgap.h"
+#include "bwtaln.h"
+
+#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_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
+{
+	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->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;
+}
+
+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 a, int i, bwtint_t k, bwtint_t l, int n_mm, int n_gapo, int n_gape,
+							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 <<= 1;
+		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
+	}
+	p = q->stack + q->n_entries;
+	p->info = (u_int32_t)score<<21 | a<<20 | i; p->k = k; p->l = l;
+	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape; p->state = state;
+	if (is_diff) p->last_diff_pos = i;
+	++(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 bwts[2], int len, const ubyte_t *seq[2], bwt_width_t *w[2],
+						  bwt_width_t *seed_w[2], const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack)
+{
+	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[0][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, 0, len, 0, bwts[0]->seq_len, 0, 0, 0, 0, 0, opt);
+	gap_push(stack, 1, len, 0, bwts[0]->seq_len, 0, 0, 0, 0, 0, opt);
+
+	while (stack->n_entries) {
+		gap_entry_t e;
+		int a, i, m, m_seed = 0, hit_found, allow_diff, allow_M, tmp;
+		bwtint_t k, l, cnt_k[4], cnt_l[4], occ;
+		const bwt_t *bwt;
+		const ubyte_t *str;
+		const bwt_width_t *seed_width = 0;
+		bwt_width_t *width;
+
+		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
+		a = e.info>>20&1; i = e.info&0xffff; // strand, 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;
+		bwt = bwts[1-a]; str = seq[a]; width = w[a];
+		if (seed_w) { // apply seeding
+			seed_width = seed_w[a];
+			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, str, &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->a = a;
+				p->k = k; p->l = l;
+				p->score = score;
+				++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_w && 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, a, i, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, 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, a, i + 1, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, 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, a, i, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, 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, a, i + 1, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_D, 1, opt);
+						}
+					}
+				}
+			}
+		}
+		// mismatches
+		if (allow_diff && allow_M) { // mismatch is allowed
+			for (j = 1; j <= 4; ++j) {
+				int c = (str[i] + j) & 3;
+				int is_mm = (j != 4 || str[i] > 3);
+				k = bwt->L2[c] + cnt_k[c] + 1;
+				l = bwt->L2[c] + cnt_l[c];
+				if (k <= l) gap_push(stack, a, i, k, l, e.n_mm + is_mm, e.n_gapo, e.n_gape, STATE_M, is_mm, opt);
+			}
+		} else if (str[i] < 4) { // try exact match only
+			int c = str[i] & 3;
+			k = bwt->L2[c] + cnt_k[c] + 1;
+			l = bwt->L2[c] + cnt_l[c];
+			if (k <= l) gap_push(stack, a, i, k, l, e.n_mm, e.n_gapo, e.n_gape, STATE_M, 0, opt);
+		}
+	}
+
+	*_n_aln = n_aln;
+	//fprintf(stderr, "max_entries = %d\n", max_entries);
+	return aln;
+}

data/ext/bwtgap.h

@@ -0,0 +1,38 @@
+#ifndef BWTGAP_H_
+#define BWTGAP_H_
+
+#include "bwt.h"
+#include "bwtaln.h"
+
+typedef struct { // recursion stack
+	u_int32_t info; // score<<21 | a<<20 | i
+	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
+	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
+	int last_diff_pos;
+} 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_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[2], int len, const ubyte_t *seq[2], bwt_width_t *w[2],
+							  bwt_width_t *seed_w[2], 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