fixed another silly bug in mpileup's indel caller

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 25e2a86a72958ff19aa41e88b6b003816678029c..0632eef7f3fb0822dd32ec08f025ddddd38204db 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -206,15 +206,15 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                        query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
                                // do alignment; this takes most of computing time for indel calling
                                sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-                                                                        (uint8_t*)query + qbeg, qend - qbeg, &ap);
+                                                                        (uint8_t*)query, qend - qbeg, &ap);
                                score[K*n_types + t] = -sc;
 /*
                                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
                                        fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
                                fputc('\n', stderr);
-                               for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[qbeg + l]], stderr);
+                               for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
                                fputc('\n', stderr);
-                               fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
+                               fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
 */
                        }
                }