Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2_aux.c @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2_aux.c Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,639 @@ +#include <stdlib.h> +#include <stdio.h> +#include <math.h> +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif +#ifdef HAVE_PTHREAD +#include <pthread.h> +#endif +#include "bntseq.h" +#include "bwt_lite.h" +#include "utils.h" +#include "bwtsw2.h" +#include "stdaln.h" +#include "kstring.h" + +#include "kseq.h" +KSEQ_INIT(gzFile, gzread) + +#include "ksort.h" +#define __left_lt(a, b) ((a).end > (b).end) +KSORT_INIT(hit, bsw2hit_t, __left_lt) + +extern unsigned char nst_nt4_table[256]; + +unsigned char nt_comp_table[256] = { + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N', + 'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N', + 'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n', + 'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', + 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N' +}; + +extern int bsw2_resolve_duphits(const bwt_t *bwt, bwtsw2_t *b, int IS); +extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level); + +bsw2opt_t *bsw2_init_opt() +{ + bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t)); + o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30; + o->bw = 50; + o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0; + o->mask_level = 0.50f; o->yita = 5.5f; o->coef = 5.5f; + o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000; + return o; +} + +void bsw2_destroy(bwtsw2_t *b) +{ + int i; + if (b == 0) return; + if (b->cigar) + for (i = 0; i < b->n; ++i) free(b->cigar[i]); + free(b->cigar); free(b->n_cigar); free(b->hits); + free(b); +} + +#define __gen_ap(par, opt) do { \ + int i; \ + for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b; \ + for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \ + (par).gap_open = (opt)->q; (par).gap_ext = (opt)->r; \ + (par).gap_end = (opt)->r; \ + (par).row = 5; (par).band_width = opt->bw; \ + } while (0) + +#define __rpac(pac, l, i) (pac[(l-i-1)>>2] >> (~(l-i-1)&3)*2 & 0x3) + +void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem) +{ + int i, matrix[25]; + bwtint_t k; + uint8_t *target = 0, *query; + AlnParam par; + + par.matrix = matrix; + __gen_ap(par, opt); + query = calloc(lq, 1); + // sort according to the descending order of query end + ks_introsort(hit, b->n, b->hits); + target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1); + // reverse _query + for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i]; + // core loop + for (i = 0; i < b->n; ++i) { + bsw2hit_t *p = b->hits + i; + int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq; + int score, j; + path_t path; + p->n_seeds = 1; + if (p->l || p->k == 0) continue; + for (j = score = 0; j < i; ++j) { + bsw2hit_t *q = b->hits + j; + if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) { + if (q->n_seeds < (1<<14) - 2) ++q->n_seeds; + ++score; + } + } + if (score) continue; + if (lt > p->k) lt = p->k; + if (is_rev) { + for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered! + target[j++] = __rpac(pac, l_pac, k); + } else { + for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered! + target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3; + } + lt = j; + score = aln_extend_core(target, lt, query + lq - p->beg, p->beg, &par, &path, 0, p->G, _mem); + if (score > p->G) { // extensible + p->G = score; + p->len += path.i; + p->beg -= path.j; + p->k -= path.i; + } + } + free(query); free(target); +} + +void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem) +{ + int i, matrix[25]; + uint32_t k; + uint8_t *target; + AlnParam par; + + par.matrix = matrix; + __gen_ap(par, opt); + target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1); + for (i = 0; i < b->n; ++i) { + bsw2hit_t *p = b->hits + i; + int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq; + int j, score; + path_t path; + if (p->l) continue; + if (is_rev) { + for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k) + target[j++] = __rpac(pac, l_pac, k); + } else { + for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k) + target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3; + } + lt = j; + score = aln_extend_core(target, lt, query + p->beg, lq - p->beg, &par, &path, 0, 1, _mem); +// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G); + if (score >= p->G) { + p->G = score; + p->len = path.i; + p->end = path.j + p->beg; + } + } + free(target); +} + +/* generate CIGAR array(s) in b->cigar[] */ +static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], uint8_t *pac, bwtsw2_t *b) +{ + uint8_t *target; + int i, matrix[25]; + AlnParam par; + path_t *path; + + par.matrix = matrix; + __gen_ap(par, opt); + i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length + target = calloc(i, 1); + path = calloc(i + lq, sizeof(path_t)); + // memory clean up for b + if (b->n < b->max) { + b->max = b->n; + b->hits = realloc(b->hits, b->n * sizeof(bsw2hit_t)); + } + if (b->cigar) free(b->cigar); + if (b->n_cigar) free(b->n_cigar); + b->cigar = (uint32_t**)calloc(b->max, sizeof(void*)); + b->n_cigar = (int*)calloc(b->max, sizeof(int)); + // generate CIGAR + for (i = 0; i < b->n; ++i) { + bsw2hit_t *p = b->hits + i; + uint8_t *query; + uint32_t k; + int score, path_len, beg, end; + if (p->l) continue; + beg = (p->flag & 0x10)? lq - p->end : p->beg; + end = (p->flag & 0x10)? lq - p->beg : p->end; + query = seq[(p->flag & 0x10)? 1 : 0] + beg; + for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here + target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3; + score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len); + b->cigar[i] = aln_path2cigar32(path, path_len, &b->n_cigar[i]); + if (beg != 0 || end < lq) { // write soft clipping + b->cigar[i] = realloc(b->cigar[i], 4 * (b->n_cigar[i] + 2)); + if (beg != 0) { + memmove(b->cigar[i] + 1, b->cigar[i], b->n_cigar[i] * 4); + b->cigar[i][0] = beg<<4 | 4; + ++b->n_cigar[i]; + } + if (end < lq) { + b->cigar[i][b->n_cigar[i]] = (lq - end)<<4 | 4; + ++b->n_cigar[i]; + } + } + } + free(target); free(path); +} + +/* this is for the debugging purpose only */ +void bsw2_debug_hits(const bwtsw2_t *b) +{ + int i; + printf("# raw hits: %d\n", b->n); + for (i = 0; i < b->n; ++i) { + bsw2hit_t *p = b->hits + i; + if (p->l == 0) + printf("%d, %d, %d, %u, %u\n", p->G, p->beg, p->end, p->k, p->l); + } +} + +static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse) +{ + int i; + if (b[0]->n + b[1]->n > b[0]->max) { + b[0]->max = b[0]->n + b[1]->n; + b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t)); + } + for (i = 0; i < b[1]->n; ++i) { + bsw2hit_t *p = b[0]->hits + b[0]->n + i; + *p = b[1]->hits[i]; + if (is_reverse) { + int x = p->beg; + p->beg = l - p->end; + p->end = l - x; + p->flag |= 0x10; + } + } + b[0]->n += b[1]->n; + bsw2_destroy(b[1]); + b[1] = 0; +} + +static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int l, uint8_t *seq[2], int is_rev, bsw2global_t *pool) +{ + extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]); + bwtsw2_t *b[2], **bb[2]; + int k; + for (k = 0; k < 2; ++k) { + bwtl_t *query = bwtl_seq2bwtl(l, seq[k]); + bb[k] = bsw2_core(opt, query, target, pool); + bwtl_destroy(query); + } + b[0] = bb[0][1]; b[1] = bb[1][1]; + bsw2_chain_filter(opt, l, b); + for (k = 0; k < 2; ++k) { + bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem); + merge_hits(bb[k], l, 0); + bsw2_resolve_duphits(0, bb[k][0], 0); + bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem); + b[k] = bb[k][0]; + free(bb[k]); + } + merge_hits(b, l, 1); + bsw2_resolve_query_overlaps(b[0], opt->mask_level); + return b[0]; +} + +/* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */ +static void flag_fr(bwtsw2_t *b[2]) +{ + int i, j; + for (i = 0; i < b[0]->n; ++i) { + bsw2hit_t *p = b[0]->hits + i; + p->flag |= 0x10000; + } + for (i = 0; i < b[1]->n; ++i) { + bsw2hit_t *p = b[1]->hits + i; + p->flag |= 0x20000; + } + for (i = 0; i < b[0]->n; ++i) { + bsw2hit_t *p = b[0]->hits + i; + for (j = 0; j < b[1]->n; ++j) { + bsw2hit_t *q = b[1]->hits + i; + if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) { + q->flag |= 0x30000; p->flag |= 0x30000; + break; + } + } + } +} + +typedef struct { + int l, tid; + char *name, *seq, *qual, *sam; +} bsw2seq1_t; + +typedef struct { + int n, max; + bsw2seq1_t *seq; +} bsw2seq_t; + +#ifdef HAVE_PTHREAD +static pthread_mutex_t g_dbwtsw_lock = PTHREAD_MUTEX_INITIALIZER; +#endif + +static int fix_cigar(const char *qname, const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar) +{ + // FIXME: this routine does not work if the query bridge three reference sequences + int32_t coor, refl, lq; + int x, y, i, seqid; + bns_coor_pac2real(bns, p->k, p->len, &seqid); + coor = p->k - bns->anns[seqid].offset; + refl = bns->anns[seqid].len; + x = coor; y = 0; + // test if the alignment goes beyond the boundary + for (i = 0; i < n_cigar; ++i) { + int op = cigar[i]&0xf, ln = cigar[i]>>4; + if (op == 1 || op == 4 || op == 5) y += ln; + else if (op == 2) x += ln; + else x += ln, y += ln; + } + lq = y; // length of the query sequence + if (x > refl) { // then fix it + int j, nc, mq[2], nlen[2]; + uint32_t *cn, kk = 0; + nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0; + cn = calloc(n_cigar + 3, 4); + x = coor; y = 0; + for (i = j = 0; i < n_cigar; ++i) { + int op = cigar[i]&0xf, ln = cigar[i]>>4; + if (op == 4 || op == 5 || op == 1) { // ins or clipping + y += ln; + cn[j++] = cigar[i]; + } else if (op == 2) { // del + if (x + ln >= refl && nc == 0) { + cn[j++] = (uint32_t)(lq - y)<<4 | 4; + nc = j; + cn[j++] = (uint32_t)y<<4 | 4; + kk = p->k + (x + ln - refl); + nlen[0] = x - coor; + nlen[1] = p->len - nlen[0] - ln; + } else cn[j++] = cigar[i]; + x += ln; + } else if (op == 0) { // match + if (x + ln >= refl && nc == 0) { + // FIXME: not consider a special case where a split right between M and I + cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M + cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S + nc = j; + mq[0] += refl - x; + cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4; + if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0; + mq[1] += x + ln - refl; + kk = bns->anns[seqid].offset + refl; + nlen[0] = refl - coor; + nlen[1] = p->len - nlen[0]; + } else { + cn[j++] = cigar[i]; + mq[nc?1:0] += ln; + } + x += ln; y += ln; + } + } + if (mq[0] > mq[1]) { // then take the first alignment + n_cigar = nc; + memcpy(cigar, cn, 4 * nc); + p->len = nlen[0]; + } else { + p->k = kk; p->len = nlen[1]; + n_cigar = j - nc; + memcpy(cigar, cn + nc, 4 * (j - nc)); + } + free(cn); + } + return n_cigar; +} + +/* generate SAM lines for a sequence in ks with alignment stored in + * b. ks->name and ks->seq will be freed and set to NULL in the end. */ +static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b) +{ + int i, k; + kstring_t str; + memset(&str, 0, sizeof(kstring_t)); + for (i = 0; i < b->n; ++i) { + bsw2hit_t *p = b->hits + i; + int32_t seqid = -1, coor = -1; + int j, qual, nn = 0; + int beg, end; + if (p->l == 0) { + b->n_cigar[i] = fix_cigar(ks->name, bns, p, b->n_cigar[i], b->cigar[i]); + nn = bns_coor_pac2real(bns, p->k, p->len, &seqid); + coor = p->k - bns->anns[seqid].offset; + } + ksprintf(&str, "%s\t%d", ks->name, p->flag&0x10); + ksprintf(&str, "\t%s\t%d", seqid>=0? bns->anns[seqid].name : "*", coor + 1); + if (p->l == 0) { + { // estimate mapping quality + float c = 1.0; + int subo = p->G2 > opt->t? p->G2 : opt->t; + if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5; + if (p->n_seeds < 2) c *= .2; + qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499); + if (qual > 250) qual = 250; + if (p->flag&1) qual = 0; + } + ksprintf(&str, "\t%d\t", qual); + for (k = 0; k < b->n_cigar[i]; ++k) + ksprintf(&str, "%d%c", b->cigar[i][k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[b->cigar[i][k]&0xf]); + } else ksprintf(&str, "\t0\t*"); + ksprintf(&str, "\t*\t0\t0\t"); + beg = 0; end = ks->l; + if (opt->hard_clip) { + if ((b->cigar[i][0]&0xf) == 4) beg += b->cigar[i][0]>>4; + if ((b->cigar[i][b->n_cigar[i]-1]&0xf) == 4) end -= b->cigar[i][b->n_cigar[i]-1]>>4; + } + for (j = beg; j < end; ++j) { + if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str); + else kputc(ks->seq[j], &str); + } + if (ks->qual) { + kputc('\t', &str); + for (j = beg; j < end; ++j) { + if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str); + else kputc(ks->qual[j], &str); + } + } else ksprintf(&str, "\t*"); + ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tXN:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, nn); + if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1); + kputc('\n', &str); + } + ks->sam = str.s; + free(ks->seq); ks->seq = 0; + free(ks->qual); ks->qual = 0; + free(ks->name); ks->name = 0; +} + +/* Core routine to align reads in _seq. It is separated from + * process_seqs() to realize multi-threading */ +static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2]) +{ + int x; + bsw2opt_t opt = *_opt; + bsw2global_t *pool = bsw2_global_init(); + for (x = 0; x < _seq->n; ++x) { + bsw2seq1_t *p = _seq->seq + x; + uint8_t *seq[2], *rseq[2]; + int i, l, k; + bwtsw2_t *b[2]; + l = p->l; + +#ifdef HAVE_PTHREAD + if (_opt->n_threads > 1) { + pthread_mutex_lock(&g_dbwtsw_lock); + if (p->tid < 0) p->tid = tid; + else if (p->tid != tid) { + pthread_mutex_unlock(&g_dbwtsw_lock); + continue; + } // in pinciple else should not happen + pthread_mutex_unlock(&g_dbwtsw_lock); + } +#endif + + // set opt->t + opt.t = _opt->t; + if (opt.t < log(l) * opt.coef) opt.t = (int)(log(l) * opt.coef + .499); + if (pool->max_l < l) { // then enlarge working space for aln_extend_core() + int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l; + pool->max_l = l; + pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24); + } + // set opt->bw + opt.bw = _opt->bw; + k = (l * opt.a - 2 * opt.q) / (2 * opt.r + opt.a); + i = (l * opt.a - opt.a - opt.t) / opt.r; + if (k > i) k = i; + if (k < 1) k = 1; // I do not know if k==0 causes troubles + opt.bw = _opt->bw < k? _opt->bw : k; + // set seq[2] and rseq[2] + seq[0] = calloc(l * 4, 1); + seq[1] = seq[0] + l; + rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l; + // convert sequences to 2-bit representation + for (i = k = 0; i < l; ++i) { + int c = nst_nt4_table[(int)p->seq[i]]; + if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled + seq[0][i] = c; + seq[1][l-1-i] = 3 - c; + rseq[0][l-1-i] = c; + rseq[1][i] = 3 - c; + } + if (l - k < opt.t) { + free(seq[0]); continue; + } + // alignment + b[0] = bsw2_aln1_core(&opt, bns, pac, target[0], l, seq, 0, pool); + for (k = 0; k < b[0]->n; ++k) + if (b[0]->hits[k].n_seeds < opt.t_seeds) break; + if (k < b[0]->n) { + b[1] = bsw2_aln1_core(&opt, bns, pac, target[1], l, rseq, 1, pool); + for (i = 0; i < b[1]->n; ++i) { + bsw2hit_t *p = b[1]->hits + i; + int x = p->beg; + p->beg = l - p->end; + p->end = l - x; + if (p->l == 0) p->k = bns->l_pac - (p->k + p->len); + } + flag_fr(b); + merge_hits(b, l, 0); + bsw2_resolve_duphits(0, b[0], 0); + bsw2_resolve_query_overlaps(b[0], opt.mask_level); + } else b[1] = 0; + // generate CIGAR and print SAM + gen_cigar(&opt, l, seq, pac, b[0]); + print_hits(bns, &opt, p, b[0]); + // free + free(seq[0]); + bsw2_destroy(b[0]); + } + bsw2_global_destroy(pool); +} + +#ifdef HAVE_PTHREAD +typedef struct { + int tid; + bsw2seq_t *_seq; + const bsw2opt_t *_opt; + const bntseq_t *bns; + uint8_t *pac; + bwt_t *target[2]; +} thread_aux_t; + +/* another interface to bsw2_aln_core() to facilitate pthread_create() */ +static void *worker(void *data) +{ + thread_aux_t *p = (thread_aux_t*)data; + bsw2_aln_core(p->tid, p->_seq, p->_opt, p->bns, p->pac, p->target); + return 0; +} +#endif + +/* process sequences stored in _seq, generate SAM lines for these + * sequences and reset _seq afterwards. */ +static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2]) +{ + int i; + +#ifdef HAVE_PTHREAD + if (opt->n_threads <= 1) { + bsw2_aln_core(0, _seq, opt, bns, pac, target); + } else { + pthread_t *tid; + pthread_attr_t attr; + thread_aux_t *data; + int j; + pthread_attr_init(&attr); + pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); + data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t)); + tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t)); + for (j = 0; j < opt->n_threads; ++j) { + thread_aux_t *p = data + j; + p->tid = j; p->_seq = _seq; p->_opt = opt; p->bns = bns; + p->pac = pac; p->target[0] = target[0]; p->target[1] = target[1]; + pthread_create(&tid[j], &attr, worker, p); + } + for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0); + free(data); free(tid); + } +#else + bsw2_aln_core(0, _seq, opt, bns, pac, target); +#endif + + // print and reset + for (i = 0; i < _seq->n; ++i) { + bsw2seq1_t *p = _seq->seq + i; + if (p->sam) printf("%s", p->sam); + free(p->name); free(p->seq); free(p->qual); free(p->sam); + p->tid = -1; p->l = 0; + p->name = p->seq = p->qual = p->sam = 0; + } + fflush(stdout); + _seq->n = 0; +} + +void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn) +{ + gzFile fp; + kseq_t *ks; + int l, size = 0; + uint8_t *pac; + bsw2seq_t *_seq; + + pac = calloc(bns->l_pac/4+1, 1); + if (pac == 0) { + fprintf(stderr, "[bsw2_aln] insufficient memory!\n"); + return; + } + for (l = 0; l < bns->n_seqs; ++l) + printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len); + fread(pac, 1, bns->l_pac/4+1, bns->fp_pac); + fp = xzopen(fn, "r"); + ks = kseq_init(fp); + _seq = calloc(1, sizeof(bsw2seq_t)); + while ((l = kseq_read(ks)) >= 0) { + bsw2seq1_t *p; + if (_seq->n == _seq->max) { + _seq->max = _seq->max? _seq->max<<1 : 1024; + _seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t)); + } + p = &_seq->seq[_seq->n++]; + p->tid = -1; + p->l = l; + p->name = strdup(ks->name.s); + p->seq = strdup(ks->seq.s); + p->qual = ks->qual.l? strdup(ks->qual.s) : 0; + p->sam = 0; + size += l; + if (size > opt->chunk_size) { + fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size); + process_seqs(_seq, opt, bns, pac, target); + size = 0; + } + } + fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size); + process_seqs(_seq, opt, bns, pac, target); + free(_seq->seq); free(_seq); + kseq_destroy(ks); + gzclose(fp); + free(pac); +}