for backup. no effective changes

diff --git a/bam2bcf.c b/bam2bcf.c
index 509761d3395df7d01e56f7a368f2f2daa29be4b3..d5a8dd440286cc2b6d0b119df6e6940d8ea05bbf 100644 (file)
--- 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 4de743a9287f7421e6f612a2426897d3dbe69212..92f104507952d5197a6bde2bd326ff16595cf558 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,13 +2,23 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
+#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 a3e6aeb614927733676b2b25e4592786cb14ef2e..ed230e8fb8c763388f57a272acee2ca5f96e7503 100644 (file)
--- 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) {