* optionally drop phase ambiguous reads

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index c157bc65b9663d62f3ede6863d55d0fe26e7e152..899428f1c8c4202caaefded876e290c37f7cb6ac 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -420,9 +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;
+                               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