* samtools-0.1.9-10 (r816)

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2e0b04dfee68f01032665345ac7961ea7ba1a059..7713b51bdb8b174510c309262f29bac6c83ce976 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -277,7 +277,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                for (l = qbeg; l < qend; ++l)
                                        query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
                                // do alignment; this is the bottleneck
-                               if (0) {
+                               if (1) {
                                        const uint8_t *qual = bam1_qual(p->b), *bq;
                                        uint8_t *qq = 0;
                                        qq = calloc(qend - qbeg, 1);
@@ -286,12 +286,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                        for (l = qbeg; l < qend; ++l) {
                                                qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
                                                if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
+                                               if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
                                        }
                                        sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
                                                                        (uint8_t*)query, qend - qbeg, qq, &apf, 0, 0);
                                        score[K*n_types + t] = sc;
                                        free(qq);
-                               } else {
+                               } else { // the following block is for testing only
                                        sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
                                                                                 (uint8_t*)query, qend - qbeg, &apv);
                                        score[K*n_types + t] = -sc;