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bugfix: wrong mapping quality

This commit is contained in:
Heng Li 2011-11-12 12:12:45 -05:00
parent b42910ada6
commit fa8cfe5567
4 changed files with 39 additions and 38 deletions
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7
bwtsw2.h
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@ -6,9 +6,10 @@
#include "bwt_lite.h" #include "bwt_lite.h"
#include "bwt.h" #include "bwt.h"
#define BSW2_FLAG_MATESW 0x100 #define BSW2_FLAG_MATESW 0x100
#define BSW2_FLAG_TANDEM 0x200 #define BSW2_FLAG_TANDEM 0x200
#define BSW2_FLAG_MOVED 0x400 #define BSW2_FLAG_MOVED 0x400
#define BSW2_FLAG_RESCUED 0x800
typedef struct { typedef struct {
int a, b, q, r, t, qr, bw; int a, b, q, r, t, qr, bw;

20
bwtsw2_aux.c
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@ -452,17 +452,15 @@ static void update_mate_aux(bwtsw2_t *b, const bwtsw2_t *m)
// update mapping quality // update mapping quality
if (b->n == 1 && m->n == 1) { if (b->n == 1 && m->n == 1) {
bsw2hit_t *p = &b->hits[0]; bsw2hit_t *p = &b->hits[0];
int isize; if (p->flag & BSW2_FLAG_MATESW) { // this alignment is found by Smith-Waterman
if (p->flag & BSW2_FLAG_MATESW) { // this alignment is rescued by Smith-Waterman if (!(p->flag & BSW2_FLAG_TANDEM) && b->aux[0].pqual < 20)
if (!(p->flag & BSW2_FLAG_TANDEM) && b->aux[0].pqual < m->aux[0].qual) b->aux[0].pqual = 20;
b->aux[0].pqual = m->aux[0].qual; if (b->aux[0].pqual >= m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
} else if (p->flag&2) { // properly paired } else if ((p->flag & 2) && !(m->hits[0].flag & BSW2_FLAG_MATESW)) { // properly paired
if (!(p->flag & BSW2_FLAG_TANDEM)) { // not around a tandem repeat if (!(p->flag & BSW2_FLAG_TANDEM)) { // pqual is bounded by [b->aux[0].qual,m->aux[0].qual]
if (b->aux[0].pqual < m->aux[0].qual) { b->aux[0].pqual += 20;
b->aux[0].pqual += 20; if (b->aux[0].pqual > m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
if (b->aux[0].pqual >= m->aux[0].qual) if (b->aux[0].pqual < b->aux[0].qual) b->aux[0].pqual = b->aux[0].qual;
b->aux[0].pqual = m->aux[0].qual;
}
} }
} }
} }

48
bwtsw2_pair.c
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@ -85,7 +85,7 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
ksw_query_t *q; ksw_query_t *q;
ksw_aux_t aux[2]; ksw_aux_t aux[2];
// compute the region start and end // compute the region start and end
a->n_seeds = 1; a->l = 0; a->n_seeds = 1; a->flag |= BSW2_FLAG_MATESW; // before calling this routine, *a has been cleared with memset(0); the flag is set with 1<<6/7
if (h->is_rev == 0) { if (h->is_rev == 0) {
beg = (int64_t)(h->k + st->avg - EXT_STDDEV * st->std - l_mseq + .499); beg = (int64_t)(h->k + st->avg - EXT_STDDEV * st->std - l_mseq + .499);
end = (int64_t)(h->k + st->avg + EXT_STDDEV * st->std + .499); end = (int64_t)(h->k + st->avg + EXT_STDDEV * st->std + .499);
@ -117,7 +117,6 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
ksw_sse2(q, end - beg, ref, &aux[0]); ksw_sse2(q, end - beg, ref, &aux[0]);
free(q); free(q);
if (aux[0].score < opt->t) { if (aux[0].score < opt->t) {
aux[0].score = 0;
free(seq); free(seq);
return; return;
} }
@ -132,6 +131,8 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
// write output // write output
a->G = aux[0].score; a->G = aux[0].score;
a->G2 = aux[0].score2 > aux[1].score2? aux[0].score2 : aux[1].score2; a->G2 = aux[0].score2 > aux[1].score2? aux[0].score2 : aux[1].score2;
if (a->G2 < opt->t) a->G2 = 0;
if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
a->k = beg + (aux[0].te - aux[1].te); a->k = beg + (aux[0].te - aux[1].te);
a->len = aux[1].te; a->len = aux[1].te;
a->beg = aux[0].qe - aux[1].qe; a->beg = aux[0].qe - aux[1].qe;
@ -174,8 +175,7 @@ void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, b
if (hits[i]->n == 1) p[0] = hits[i], p[1] = hits[i+1], which = 1; if (hits[i]->n == 1) p[0] = hits[i], p[1] = hits[i+1], which = 1;
else p[0] = hits[i+1], p[1] = hits[i], which = 0; else p[0] = hits[i+1], p[1] = hits[i], which = 0;
if (a[which].G == 0) continue; if (a[which].G == 0) continue;
a[which].flag |= BSW2_FLAG_MATESW; a[which].flag |= BSW2_FLAG_RESCUED;
if (a[which].G2) a[which].flag |= BSW2_FLAG_TANDEM;
if (p[1]->max == 0) { if (p[1]->max == 0) {
p[1]->max = 1; p[1]->max = 1;
p[1]->hits = malloc(sizeof(bsw2hit_t)); p[1]->hits = malloc(sizeof(bsw2hit_t));
@ -186,30 +186,31 @@ void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, b
p[1]->hits[0].flag |= 2; p[1]->hits[0].flag |= 2;
++n_rescued; ++n_rescued;
} else { // then both ends mapped } else { // then both ends mapped
int ori_G2[2]; int is_fixed = 0;
//fprintf(stderr, "%d; %lld,%lld; %d,%d\n", a[0].is_rev, hits[i]->hits[0].k, a[0].k, hits[i]->hits[0].end, a[0].end); //fprintf(stderr, "%d; %lld,%lld; %d,%d\n", a[0].is_rev, hits[i]->hits[0].k, a[0].k, hits[i]->hits[0].end, a[0].end);
ori_G2[0] = a[0].G2; ori_G2[1] = a[1].G2; for (j = 0; j < 2; ++j) { // fix wrong mappings and wrong suboptimal alignment score
for (j = 0; j < 2; ++j) { // first fix wrong mappings bsw2hit_t *p = &hits[i+j]->hits[0];
if (hits[i+j]->hits[0].G < a[j].G) { // the orginal mapping is suboptimal if (p->G < a[j].G) { // the orginal mapping is suboptimal
a[j].G2 = a[j].G2 > hits[i+j]->hits[0].G? a[j].G2 : hits[i+j]->hits[0].G; a[j].G2 = a[j].G2 > p->G? a[j].G2 : p->G; // FIXME: reset BSW2_FLAG_TANDEM?
hits[i+j]->hits[0] = a[j]; *p = a[j];
++n_fixed; ++n_fixed;
is_fixed = 1;
} else if (p->k != a[j].k && p->G2 < a[j].G) {
p->G2 = a[j].G;
} else if (p->k == a[j].k && p->G2 < a[j].G2) {
p->G2 = a[j].G2;
} }
} }
if (hits[i]->hits[0].k == a[0].k && hits[i+1]->hits[0].k == a[1].k) { // properly paired and no ends need to be moved if (hits[i]->hits[0].k == a[0].k && hits[i+1]->hits[0].k == a[1].k) { // properly paired and no ends need to be moved
for (j = 0; j < 2; ++j) { for (j = 0; j < 2; ++j)
if (hits[i+j]->hits[0].G2 < a[j].G2) hits[i+j]->hits[0].flag |= 2 | (a[j].flag & BSW2_FLAG_TANDEM);
hits[i+j]->hits[0].G2 = a[j].G2;
if (ori_G2[j]) hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM;
hits[i+j]->hits[0].flag |= 2;
}
} else if (hits[i]->hits[0].k == a[0].k || hits[i+1]->hits[0].k == a[1].k) { // a tandem match } else if (hits[i]->hits[0].k == a[0].k || hits[i+1]->hits[0].k == a[1].k) { // a tandem match
for (j = 0; j < 2; ++j) { for (j = 0; j < 2; ++j) {
hits[i+j]->hits[0].flag |= 2; hits[i+j]->hits[0].flag |= 2;
if (hits[i+j]->hits[0].k != a[j].k) if (hits[i+j]->hits[0].k != a[j].k)
hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM; hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM;
} }
} else if (a[0].G || a[1].G) { // it is possible to move one end } else if (!is_fixed && (a[0].G || a[1].G)) { // it is possible to move one end
if (a[0].G && a[1].G) { // now we have two "proper pairs" if (a[0].G && a[1].G) { // now we have two "proper pairs"
int G[2]; int G[2];
double diff; double diff;
@ -219,7 +220,7 @@ void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, b
if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0; if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0;
} }
if (a[0].G == 0 || a[1].G == 0) { // one proper pair only if (a[0].G == 0 || a[1].G == 0) { // one proper pair only
bsw2hit_t *p[2]; bsw2hit_t *p[2]; // p[0] points the unchanged hit; p[1] to the hit to be moved
int which, isize; int which, isize;
double dev, diff; double dev, diff;
if (a[0].G) p[0] = &hits[i+1]->hits[0], p[1] = &hits[i]->hits[0], which = 0; if (a[0].G) p[0] = &hits[i+1]->hits[0], p[1] = &hits[i]->hits[0], which = 0;
@ -227,16 +228,17 @@ void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, b
isize = p[0]->is_rev? p[0]->k + p[0]->len - a[which].k : a[which].k + a[which].len - p[0]->k; isize = p[0]->is_rev? p[0]->k + p[0]->len - a[which].k : a[which].k + a[which].len - p[0]->k;
dev = fabs(isize - pes.avg) / pes.std; dev = fabs(isize - pes.avg) / pes.std;
diff = (double)(p[1]->G - a[which].G) / (opt->a + opt->b) / (p[1]->end - p[1]->beg) * 100.0; diff = (double)(p[1]->G - a[which].G) / (opt->a + opt->b) / (p[1]->end - p[1]->beg) * 100.0;
if (diff < dev * 2.) { // then move if (diff < dev * 2.) { // then move (heuristic)
int tflag = 0;
if (ori_G2[which]) tflag = BSW2_FLAG_TANDEM;
a[which].G2 = a[which].G; a[which].G2 = a[which].G;
p[1][0] = a[which]; p[1][0] = a[which];
p[1]->flag |= BSW2_FLAG_MOVED | 2 | tflag; p[1]->flag |= BSW2_FLAG_MOVED | 2;
p[0]->flag |= 2; p[0]->flag |= 2;
++n_moved; ++n_moved;
} }
} // else, do nothing }
} else if (is_fixed) {
hits[i+0]->hits[0].flag |= 2;
hits[i+1]->hits[0].flag |= 2;
} }
} }
} }

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-r78-dev" #define PACKAGE_VERSION "0.6.0-r79-dev"
#endif #endif
static int usage() static int usage()