From 98946f7c4842bc7c0429bb78982366ce46c70624 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 5 Nov 2010 02:58:43 +0000 Subject: [PATCH] for backup. no effective changes --- bam2bcf.c | 115 ++++++++++++++++++++++++++++++++++++++++++++++++---- bam2bcf.h | 17 ++++++-- bam_plcmd.c | 15 +++++++ 3 files changed, 136 insertions(+), 11 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 509761d..d5a8dd4 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -3,7 +3,6 @@ #include "bam.h" #include "kstring.h" #include "bam2bcf.h" -#include "errmod.h" #include "bcftools/bcf.h" extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); @@ -14,18 +13,15 @@ extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CAP_DIST 25 -struct __bcf_callaux_t { - int max_bases, capQ, min_baseQ; - uint16_t *bases; - errmod_t *e; -}; - bcf_callaux_t *bcf_call_init(double theta, int min_baseQ) { bcf_callaux_t *bca; if (theta <= 0.) theta = CALL_DEFTHETA; bca = calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; + bca->openQ = 40; + bca->extQ = 20; + bca->tandemQ = 100; bca->min_baseQ = min_baseQ; bca->e = errmod_init(1. - theta); return bca; @@ -57,7 +53,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf const bam_pileup1_t *p = pl + i; int q, b, mapQ, baseQ, is_diff, min_dist; // set base - if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases + if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality if (q < bca->min_baseQ) continue; mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; @@ -87,6 +83,109 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf return r->depth; } +int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r) +{ + int i, n, n_ins, n_del; + memset(r, 0, sizeof(bcf_callret1_t)); + if (_n == 0) return -1; + + // enlarge the bases array if necessary + if (bca->max_bases < _n) { + bca->max_bases = _n; + kroundup32(bca->max_bases); + bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); + } + // fill the bases array + memset(r, 0, sizeof(bcf_callret1_t)); + r->indelreg = 10000; + for (i = n = 0; i < _n; ++i) { + const bam_pileup1_t *p = pl + i; + int q, b, mapQ, indelQ, is_diff, min_dist; + if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; + { // compute indel (base) quality + // this can be made more efficient, but realignment is the bottleneck anyway + int j, k, x, y, op, len = 0, max_left, max_rght, seqQ, indelreg; + bam1_core_t *c = &p->b->core; + uint32_t *cigar = bam1_cigar(p->b); + uint8_t *qual = bam1_qual(p->b); + for (k = y = 0, x = c->pos; k < c->n_cigar && y <= p->qpos; ++k) { + op = cigar[k]&0xf; + len = cigar[k]>>4; + if (op == BAM_CMATCH) { + if (pos > x && pos < x + len) break; + x += len; y += len; + } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += len; + else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += len; + } + if (k == c->n_cigar) continue; // this actually should not happen + max_left = max_rght = 0; indelreg = 0; + if (pos == x + len - 1 && k+2 < c->n_cigar && ((cigar[k+1]&0xf) == BAM_CINS || (cigar[k+1]&0xf) == BAM_CDEL) + && (cigar[k+2]&0xf) == BAM_CMATCH) + { + for (j = y; j < y + len; ++j) + if (max_left < qual[j]) max_left = qual[j]; + if ((cigar[k+1]&0xf) == BAM_CINS) y += cigar[k+1]>>4; + else x += cigar[k+1]>>4; + op = cigar[k+2]&0xf; len = cigar[k+2]>>4; + for (j = y; j < y + len; ++j) { + if (max_rght < qual[j]) max_rght = qual[j]; + if (qual[j] > BAM2BCF_INDELREG_THRES && indelreg == 0) + indelreg = j - y + 1; + } + } else { + for (j = y; j <= p->qpos; ++j) + if (max_left < qual[j]) max_left = qual[j]; + for (j = p->qpos + 1; j < y + len; ++j) + if (max_rght < qual[j]) max_rght = qual[j]; + + } + indelQ = max_left < max_rght? max_left : max_rght; + // estimate the sequencing error rate + seqQ = bca->openQ; + if (p->indel != 0) seqQ += bca->extQ * (abs(p->indel) - 1); // FIXME: better to model homopolymer + if (p->indel != 0) { // a different model for tandem repeats + uint8_t *seq = bam1_seq(p->b); + int tandemQ, qb = bam1_seqi(seq, p->qpos), l; + for (j = p->qpos + 1; j < c->l_qseq; ++j) + if (qb != bam1_seqi(seq, j)) break; + l = j; + for (j = (int)p->qpos - 1; j >= 0; --j) + if (qb != bam1_seqi(seq, j)) break; + l = l - (j + 1); + tandemQ = (int)((double)(abs(p->indel)) / l * bca->tandemQ + .499); + if (seqQ > tandemQ) seqQ = tandemQ; + } +// fprintf(stderr, "%s\t%d\t%d\t%d\t%d\t%d\t%d\n", bam1_qname(p->b), pos+1, p->indel, indelQ, seqQ, max_left, max_rght); + if (indelQ > seqQ) indelQ = seqQ; + q = indelQ; + } + if (q < bca->min_baseQ) continue; + mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; + if (q > mapQ) q = mapQ; + if (q > 63) q = 63; + if (q < 4) q = 4; + b = p->indel? 1 : 0; + bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b; + // collect annotations + r->qsum[b] += q; + is_diff = b; + ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)]; + min_dist = p->b->core.l_qseq - 1 - p->qpos; + if (min_dist > p->qpos) min_dist = p->qpos; + if (min_dist > CAP_DIST) min_dist = CAP_DIST; + r->anno[1<<2|is_diff<<1|0] += indelQ; + r->anno[1<<2|is_diff<<1|1] += indelQ * indelQ; + r->anno[2<<2|is_diff<<1|0] += mapQ; + r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ; + r->anno[3<<2|is_diff<<1|0] += min_dist; + r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist; + } + r->depth = n; + // glfgen + errmod_cal(bca->e, n, 2, bca->bases, r->p); + return r->depth; +} + int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call) { int ref4, i, j, qsum[4]; diff --git a/bam2bcf.h b/bam2bcf.h index 4de743a..92f1045 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -2,13 +2,23 @@ #define BAM2BCF_H #include +#include "errmod.h" #include "bcftools/bcf.h" -struct __bcf_callaux_t; -typedef struct __bcf_callaux_t bcf_callaux_t; +#define BAM2BCF_INDELREG_THRES 13 + +typedef struct __bcf_callaux_t { + int max_bases, capQ, min_baseQ; + int openQ, extQ, tandemQ; + // for internal uses + uint16_t *bases; + errmod_t *e; +} bcf_callaux_t; typedef struct { - int depth, qsum[4]; + int depth; + float indelreg, ins_len, del_len; + int qsum[4]; int anno[16]; float p[25]; } bcf_callret1_t; @@ -29,6 +39,7 @@ extern "C" { int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r); int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call); int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP); + int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r); #ifdef __cplusplus } diff --git a/bam_plcmd.c b/bam_plcmd.c index a3e6aeb..ed230e8 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -729,6 +729,21 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP)); bcf_write(bp, bh, b); bcf_destroy(b); + // test if there is an indel + if (conf->flag&MPLP_REALN) { + for (i = 0; i < gplp.n; ++i) { + int j; + for (j = 0; j < gplp.n_plp[i]; ++j) { + const bam_pileup1_t *p = gplp.plp[i] + j; + if (p->indel != 0) break; + } + if (j != gplp.n_plp[i]) break; + } + if (i < gplp.n) { // at least one of the read contains a gap + for (i = 0; i < gplp.n; ++i) + bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i); + } + } } else { printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { -- 2.39.2