Merge branch 'master' into master_fixes. Merged up to r389.
Conflicts: bwamem.c kopen.c
This commit is contained in:
Rob Davies
commit
e88529687f
3
NEWS
3
NEWS
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@ -2,8 +2,7 @@ Release 0.7.4 (23 April, 2013)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is a bugfix release. Most of bugs are considered to be minor which only
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very rarely.
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ccur
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occur very rarely.
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* Bugfix: wrong CIGAR when a query sequence bridges three or more target
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sequences. This only happens when aligning reads to short assembly contigs.
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23
bwamem.c
23
bwamem.c
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@ -951,7 +951,7 @@ static void *worker2(void *data)
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return 0;
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}
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs)
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs, const mem_pestat_t *pes0)
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{
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int i;
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worker_t *w;
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@ -967,29 +967,30 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
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p->seqs = seqs; p->regs = regs;
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p->pes = &pes[0];
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}
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#ifdef HAVE_PTHREAD
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if (opt->n_threads == 1) {
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#endif
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worker1(w);
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if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
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if (opt->flag&MEM_F_PE) { // paired-end mode
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if (pes0) memcpy(pes, pes0, 4 * sizeof(mem_pestat_t)); // if pes0 != NULL, set the insert-size distribution as pes0
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else mem_pestat(opt, bns->l_pac, n, regs, pes); // otherwise, infer the insert size distribution from data
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}
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worker2(w);
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#ifdef HAVE_PTHREAD
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} else {
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pthread_t *tid;
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tid = (pthread_t*)xcalloc(opt->n_threads, sizeof(pthread_t));
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for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker1, &w[i]);
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for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
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if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
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if (opt->flag&MEM_F_PE) {
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if (pes0) memcpy(pes, pes0, 4 * sizeof(mem_pestat_t));
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else mem_pestat(opt, bns->l_pac, n, regs, pes);
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}
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for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker2, &w[i]);
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for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
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free(tid);
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}
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#else
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worker1(w);
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if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
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worker2(w);
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#endif
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for (i = 0; i < n; ++i) {
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err_fputs(seqs[i].sam, stdout);
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free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
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}
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free(regs); free(w);
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}
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9
bwamem.h
9
bwamem.h
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@ -57,8 +57,9 @@ typedef struct {
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typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
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typedef struct {
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int low, high, failed;
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double avg, std;
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int low, high; // lower and upper bounds within which a read pair is considered to be properly paired
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int failed; // non-zero if the orientation is not supported by sufficient data
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double avg, std; // mean and stddev of the insert size distribution
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} mem_pestat_t;
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typedef struct { // This struct is only used for the convenience of API.
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@ -103,8 +104,10 @@ extern "C" {
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* @param pac 2-bit encoded reference
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* @param n number of query sequences
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* @param seqs query sequences; $seqs[i].seq/sam to be modified after the call
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* @param pes0 insert-size info; if NULL, infer from data; if not NULL, it should be an array with 4 elements,
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* corresponding to each FF, FR, RF and RR orientation. See mem_pestat() for more info.
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*/
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs);
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void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs, const mem_pestat_t *pes0);
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/**
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* Find the aligned regions for one query sequence
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9
bwase.c
9
bwase.c
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@ -181,6 +181,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
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rb = re - tle; rlen = tle;
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seq_reverse(len, seq, 0);
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seq_reverse(rlen, rseq, 0);
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if (rlen == 0) goto refine_gapped_err;
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ksw_global(qle, &seq[len-qle], rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32);
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if (qle < len) { // write soft clip
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cigar = xrealloc(cigar, (*n_cigar + 1) * 4);
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@ -195,6 +196,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
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ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, >le, &gscore, 0);
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if (gscore > 0) tle = gtle, qle = len;
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re = rb + tle; rlen = tle;
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if (rlen == 0) goto refine_gapped_err;
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ksw_global(qle, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension
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if (qle < len) {
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cigar = xrealloc(cigar, (*n_cigar + 1) * 4);
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@ -209,6 +211,11 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
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cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
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free(rseq);
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return cigar;
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refine_gapped_err:
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free(rseq);
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*n_cigar = 0;
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return 0;
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}
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char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
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@ -320,6 +327,7 @@ void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t
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}
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if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
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s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos, &s->n_cigar, s->strand);
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if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
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}
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// generate MD tag
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str = (kstring_t*)xcalloc(1, sizeof(kstring_t));
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@ -475,6 +483,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
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for (i = 0; i < p->n_multi; ++i) {
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bwt_multi1_t *q = p->multi + i;
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int k;
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if (q->cigar == 0) continue;
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j = pos_end_multi(q, p->len) - q->pos;
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nn = bns_cnt_ambi(bns, q->pos, j, &seqid);
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err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
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16
fastmap.c
16
fastmap.c
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@ -91,9 +91,12 @@ int main_mem(int argc, char *argv[])
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bwa_fill_scmat(opt->a, opt->b, opt->mat);
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if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
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bwa_print_sam_hdr(idx->bns, rg_line);
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ko = kopen(argv[optind + 1], &fd);
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if (ko == 0) {
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if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 1]);
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return 1;
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}
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fp = gzdopen(fd, "r");
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ks = kseq_init(fp);
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if (optind + 2 < argc) {
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@ -102,11 +105,16 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__);
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} else {
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ko2 = kopen(argv[optind + 2], &fd2);
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if (ko2 == 0) {
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if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 2]);
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return 1;
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}
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fp2 = gzdopen(fd2, "r");
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ks2 = kseq_init(fp2);
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opt->flag |= MEM_F_PE;
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}
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}
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bwa_print_sam_hdr(idx->bns, rg_line);
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while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
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int64_t size = 0;
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if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
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@ -121,7 +129,11 @@ int main_mem(int argc, char *argv[])
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for (i = 0; i < n; ++i) size += seqs[i].l_seq;
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if (bwa_verbose >= 3)
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fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
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mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n, seqs);
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mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n, seqs, 0);
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for (i = 0; i < n; ++i) {
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err_fputs(seqs[i].sam, stdout);
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free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
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}
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free(seqs);
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}
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4
kopen.c
4
kopen.c
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@ -319,14 +319,14 @@ void *kopen(const char *fn, int *_fd)
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#else
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*_fd = open(fn, O_RDONLY);
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#endif
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if (*_fd) {
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if (*_fd >= 0) {
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aux = xcalloc(1, sizeof(koaux_t));
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aux->type = KO_FILE;
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aux->fd = *_fd;
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}
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}
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}
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*_fd = aux->fd;
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if (aux) *_fd = aux->fd;
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return aux;
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}
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4
main.c
4
main.c
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@ -3,7 +3,7 @@
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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "0.7.4-r385"
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#define PACKAGE_VERSION "0.7.4-r389-beta"
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#endif
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int bwa_fa2pac(int argc, char *argv[]);
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@ -92,5 +92,5 @@ int main(int argc, char *argv[])
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fprintf(stderr, " %s", argv[i]);
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fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
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}
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return 0;
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return ret;
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}
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