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r848: tag alignments with primary ALT

This commit is contained in:
Heng Li 2014-09-16 18:52:49 -04:00
parent a458442b24
commit 6f37c14f26
3 changed files with 6 additions and 2 deletions
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4
bwamem.c
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@ -880,11 +880,13 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
for (i = 0; i < n; ++i) for (i = 0; i < n; ++i)
if (i != which && !(list[i].flag&0x100)) break; if (i != which && !(list[i].flag&0x100)) break;
if (i < n) { // there are other primary hits; output them if (i < n) { // there are other primary hits; output them
int has_pri_alt = 0;
kputsn("\tSA:Z:", 6, str); kputsn("\tSA:Z:", 6, str);
for (i = 0; i < n; ++i) { for (i = 0; i < n; ++i) {
const mem_aln_t *r = &list[i]; const mem_aln_t *r = &list[i];
int k; int k;
if (i == which || (list[i].flag&0x100)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit if (i == which || (list[i].flag&0x100)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
if (list[i].is_alt) has_pri_alt = 1;
kputs(bns->anns[r->rid].name, str); kputc(',', str); kputs(bns->anns[r->rid].name, str); kputc(',', str);
kputl(r->pos+1, str); kputc(',', str); kputl(r->pos+1, str); kputc(',', str);
kputc("+-"[r->is_rev], str); kputc(',', str); kputc("+-"[r->is_rev], str); kputc(',', str);
@ -895,6 +897,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
kputc(',', str); kputw(r->NM, str); kputc(',', str); kputw(r->NM, str);
kputc(';', str); kputc(';', str);
} }
if (has_pri_alt) kputsn("\tpa:A:Y", 7, str);
} }
} }
if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); } if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
@ -1094,6 +1097,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
assert(a.rid == ar->rid); assert(a.rid == ar->rid);
a.pos = pos - bns->anns[a.rid].offset; a.pos = pos - bns->anns[a.rid].offset;
a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub; a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
a.is_alt = ar->is_alt;
free(query); free(query);
return a; return a;
} }

2
bwamem.h
View File

@ -85,7 +85,7 @@ typedef struct { // This struct is only used for the convenience of API.
int64_t pos; // forward strand 5'-end mapping position int64_t pos; // forward strand 5'-end mapping position
int rid; // reference sequence index in bntseq_t; <0 for unmapped int rid; // reference sequence index in bntseq_t; <0 for unmapped
int flag; // extra flag int flag; // extra flag
uint32_t is_rev:1, mapq:8, NM:23; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance uint32_t is_rev:1, is_alt:1, mapq:8, NM:22; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance
int n_cigar; // number of CIGAR operations int n_cigar; // number of CIGAR operations
uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234 uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234
char *XA; // alternative mappings char *XA; // alternative mappings

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r845-dirty" #define PACKAGE_VERSION "0.7.10-r848-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);