Release samtools-0.1.15 (r949:203)

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 3a8782b9e473b2fdc76c779468cfa98547d1caa8..899428f1c8c4202caaefded876e290c37f7cb6ac 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -195,8 +195,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         * sequence realignment helps to increase the power.
         */
        { // construct per-sample consensus
-               int L = right - left + 1;
-               uint32_t *cns;
+               int L = right - left + 1, max_i, max2_i;
+               uint32_t *cns, max, max2;
                char *ref0, *r;
                ref_sample = calloc(n, sizeof(void*));
                cns = calloc(L, 4);
@@ -226,8 +226,16 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                }
                        }
                        // determine the consensus
-                       for (i = 0; i < right - left; ++i)
-                               r[i] = (cns[i] && (double)(cns[i]&0xffff) / ((cns[i]&0xffff)+(cns[i]>>16&0xffff)) < 0.7)? 15 : ref0[i];
+                       for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+                       max = max2 = 0; max_i = max2_i = -1;
+                       for (i = 0; i < right - left; ++i) {
+                               if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+                               else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+                       }
+                       if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+                       if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
+                       if (max_i >= 0) r[max_i] = 15;
+                       if (max2_i >= 0) r[max2_i] = 15;
 //                     for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
                }
                free(ref0); free(cns);
@@ -310,8 +318,14 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                        // align each read to ref2
                        for (i = 0; i < n_plp[s]; ++i, ++K) {
                                bam_pileup1_t *p = plp[s] + i;
-                               int qbeg, qend, tbeg, tend, sc;
+                               int qbeg, qend, tbeg, tend, sc, kk;
                                uint8_t *seq = bam1_seq(p->b);
+                               uint32_t *cigar = bam1_cigar(p->b);
+                               if (p->b->core.flag&4) continue; // unmapped reads
+                               // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
+                               for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+                                       if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
+                               if (kk < p->b->core.n_cigar) continue;
                                // FIXME: the following skips soft clips, but using them may be more sensitive.
                                // determine the start and end of sequences for alignment
                                qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left,  0, &tbeg);
@@ -406,9 +420,11 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
                                // pick the smaller between indelQ1 and indelQ2
                                indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
-                               p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
+                               if (indelQ > 255) indelQ = 255;
+                               if (seqQ > 255) seqQ = 255;
+                               p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
                                sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
-//                             fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ);
+//                             fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
                        }
                }
                // determine bca->indel_types[] and bca->inscns