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output the NM tag

This commit is contained in:
Heng Li 2011-11-24 11:51:38 -05:00
parent 717959e819
commit b5170e0efa
3 changed files with 28 additions and 5 deletions
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2
bwtsw2.h
View File

@ -26,7 +26,7 @@ typedef struct {
} bsw2hit_t; } bsw2hit_t;
typedef struct { typedef struct {
int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize; int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
uint32_t *cigar; uint32_t *cigar;
} bsw2aux_t; } bsw2aux_t;

29
bwtsw2_aux.c
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@ -165,7 +165,7 @@ void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq,
} }
/* generate CIGAR array(s) in b->cigar[] */ /* 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) static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b)
{ {
uint8_t *target; uint8_t *target;
int i, matrix[25]; int i, matrix[25];
@ -392,7 +392,28 @@ static int fix_cigar(const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *c
return n_cigar; return n_cigar;
} }
static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8_t *seq[2], uint8_t *pac, bwtsw2_t *b) static int compute_nm(bsw2hit_t *p, int n_cigar, const uint32_t *cigar, const uint8_t *pac, const uint8_t *seq)
{
int k, x, n_mm = 0, i, n_gap = 0;
bwtint_t y;
x = 0; y = p->k;
for (k = 0; k < n_cigar; ++k) {
int op = cigar[k]&0xf;
int len = cigar[k]>>4;
if (op == 0) { // match
for (i = 0; i < len; ++i) {
int ref = pac[(y+i)>>2] >> (~(y+i)&3)*2 & 0x3;
if (seq[x + i] != ref) ++n_mm;
}
x += len; y += len;
} else if (op == 1) x += len, n_gap += len;
else if (op == 2) y += len, n_gap += len;
else if (op == 4) x += len;
}
return n_mm + n_gap;
}
static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b)
{ {
int i; int i;
// allocate for b->aux // allocate for b->aux
@ -415,6 +436,8 @@ static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8
int subo; int subo;
// fix out-of-boundary CIGAR // fix out-of-boundary CIGAR
q->n_cigar = fix_cigar(bns, p, q->n_cigar, q->cigar); q->n_cigar = fix_cigar(bns, p, q->n_cigar, q->cigar);
// compute the NM tag
q->nm = compute_nm(p, q->n_cigar, q->cigar, pac, seq[p->is_rev]);
// compute mapQ // compute mapQ
subo = p->G2 > opt->t? p->G2 : opt->t; subo = p->G2 > opt->t? p->G2 : opt->t;
if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5; if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
@ -517,7 +540,7 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
} }
} else ksprintf(&str, "\t*"); } else ksprintf(&str, "\t*");
// print optional tags // print optional tags
ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds); ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tNM:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, q->nm);
if (q->nn) ksprintf(&str, "\tXN:i:%d", q->nn); if (q->nn) ksprintf(&str, "\tXN:i:%d", q->nn);
if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1); if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
if (p->flag&BSW2_FLAG_MATESW) type |= 1; if (p->flag&BSW2_FLAG_MATESW) type |= 1;

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 "0.6.0-r97-dev" #define PACKAGE_VERSION "0.6.0-r100-dev"
#endif #endif
static int usage() static int usage()