conform to the latest (unpublished) SAM spec
for chimeric alignments
This commit is contained in:
Heng Li
parent
9a6abe51b6
commit
9735d7a31a
1
Makefile
1
Makefile
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@ -1,4 +1,5 @@
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CC= gcc
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#CC= clang --analyze
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CFLAGS= -g -Wall -O2
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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AR= ar
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6
bwa.c
6
bwa.c
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@ -185,12 +185,8 @@ int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns,
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} else abort(); // should not be here
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}
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free(cigar);
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if (*qb == *qe || *rb == *re) { // TODO: this may happen in theory, but should be very very rare...
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fprintf(stderr, "[E::%s] If you see this message, please let the developer know. Sorry.\n", __func__);
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exit(1);
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}
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}
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return 0;
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return (*qb == *qe || *rb == *re)? -2 : 0;
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}
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/*********************
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55
bwamem.c
55
bwamem.c
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@ -671,7 +671,9 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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kputw(p->mapq, str); kputc('\t', str); // MAPQ
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if (p->n_cigar) { // aligned
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for (i = 0; i < p->n_cigar; ++i) {
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kputw(p->cigar[i]>>4, str); kputc("MIDSH"[p->cigar[i]&0xf], str);
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int c = p->cigar[i]&0xf;
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if (c == 3 || c == 4) c = which? 4 : 3; // use hard clipping for supplementary alignments
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kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
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}
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} else kputc('*', str); // having a coordinate but unaligned (e.g. when copy_mate is true)
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} else kputsn("*\t0\t0\t*", 7, str); // without coordinte
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@ -698,8 +700,8 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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} else if (!p->is_rev) { // the forward strand
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int i, qb = 0, qe = s->l_seq;
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if (p->n_cigar) {
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if ((p->cigar[0]&0xf) == 4) qb += p->cigar[0]>>4;
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if ((p->cigar[p->n_cigar-1]&0xf) == 4) qe -= p->cigar[p->n_cigar-1]>>4;
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if (which && ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3)) qb += p->cigar[0]>>4;
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if (which && ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3)) qe -= p->cigar[p->n_cigar-1]>>4;
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}
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ks_resize(str, str->l + (qe - qb) + 1);
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for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
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@ -730,23 +732,25 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
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if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
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if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
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for (i = 0; i < n; ++i)
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if (i != which && !(list[i].flag&0x20000)) break; // 0x20000: shadowed multi hit
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if (i < n) { // there are other primary hits; output them
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kputsn("\tXP:Z:", 6, str);
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for (i = 0; i < n; ++i) {
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const mem_aln_t *r = &list[i];
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int k;
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if (i == which || (list[i].flag&0x20000)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
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kputs(bns->anns[r->rid].name, str); kputc(',', str);
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kputc("+-"[r->is_rev], str);
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kputl(r->pos+1, str); kputc(',', str);
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for (k = 0; k < r->n_cigar; ++k) {
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kputw(r->cigar[k]>>4, str); kputc("MIDSH"[r->cigar[k]&0xf], str);
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if (!(p->flag & 0x20000)) { // not multi-hit
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for (i = 0; i < n; ++i)
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if (i != which && !(list[i].flag&0x20000)) break; // 0x20000: shadowed multi hit
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if (i < n) { // there are other primary hits; output them
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kputsn("\tSP:Z:", 6, str);
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for (i = 0; i < n; ++i) {
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const mem_aln_t *r = &list[i];
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int k;
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if (i == which || (list[i].flag&0x20000)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
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kputs(bns->anns[r->rid].name, str); kputc(',', str);
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kputl(r->pos+1, str); kputc(',', str);
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kputc("+-"[r->is_rev], str); kputc(',', str);
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for (k = 0; k < r->n_cigar; ++k) {
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kputw(r->cigar[k]>>4, str); kputc("MIDSH"[r->cigar[k]&0xf], str);
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}
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kputc(',', str); kputw(r->mapq, str);
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kputc(',', str); kputw(r->NM, str);
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kputc(';', str);
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}
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kputc(',', str); kputw(r->mapq, str);
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kputc(',', str); kputw(r->NM, str);
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kputc(';', str);
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}
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}
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if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
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@ -791,7 +795,8 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
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*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
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q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
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if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
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if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
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if (k && p->secondary < 0) // if supplementary
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q->flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
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if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
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}
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if (aa.n == 0) { // no alignments good enough; then write an unaligned record
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@ -866,9 +871,9 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
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query[i] = query_[i] < 5? query_[i] : nst_nt4_table[(int)query_[i]];
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a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
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if (ar->secondary >= 0) a.flag |= 0x20000;
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if (bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) { // unfixable cross-reference alignment
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a.rid = -1; a.pos = -1; a.flag |= 0x4;
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return a;
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if (bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) {
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fprintf(stderr, "[E::%s] If you see this message, please let the developer know. Abort. Sorry.\n", __func__);
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exit(1);
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}
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w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
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w2 = w2 < opt->w? w2 : opt->w;
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@ -890,10 +895,10 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
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a.cigar = realloc(a.cigar, 4 * (a.n_cigar + 2));
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if (clip5) {
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memmove(a.cigar+1, a.cigar, a.n_cigar * 4);
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a.cigar[0] = clip5<<4 | (opt->flag&MEM_F_HARDCLIP? 4 : 3);
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a.cigar[0] = clip5<<4 | 3;
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++a.n_cigar;
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}
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if (clip3) a.cigar[a.n_cigar++] = clip3<<4 | (opt->flag&MEM_F_HARDCLIP? 4 : 3);
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if (clip3) a.cigar[a.n_cigar++] = clip3<<4 | 3;
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}
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a.rid = bns_pos2rid(bns, pos);
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a.pos = pos - bns->anns[a.rid].offset;
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1
bwamem.h
1
bwamem.h
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@ -11,7 +11,6 @@
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struct __smem_i;
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typedef struct __smem_i smem_i;
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#define MEM_F_HARDCLIP 0x1
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#define MEM_F_PE 0x2
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#define MEM_F_NOPAIRING 0x4
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#define MEM_F_ALL 0x8
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@ -39,7 +39,6 @@ int main_mem(int argc, char *argv[])
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else if (c == 'U') opt->pen_unpaired = atoi(optarg);
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else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
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else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
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else if (c == 'H') opt->flag |= MEM_F_HARDCLIP;
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else if (c == 'a') opt->flag |= MEM_F_ALL;
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else if (c == 'p') opt->flag |= MEM_F_PE;
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else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
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@ -82,7 +81,6 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
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fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
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fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
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fprintf(stderr, " -H hard clipping\n");
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fprintf(stderr, " -M mark shorter split hits as secondary (for Picard/GATK compatibility)\n");
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fprintf(stderr, "\nNote: Please read the man page for detailed description of the command line and options.\n");
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fprintf(stderr, "\n");
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