Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt...

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2fdee9f75a2261266912b7fe355e9ea51892ff6d..5142b3e100aa96a7ab598a95b9953aa4c6034289 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -66,7 +66,7 @@ static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos,
        for (k = 0; k < c->n_cigar; ++k) {
                int op = cigar[k] & BAM_CIGAR_MASK;
                int l = cigar[k] >> BAM_CIGAR_SHIFT;
-               if (op == BAM_CMATCH) {
+               if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
                        if (c->pos > tpos) return y;
                        if (x + l > tpos) {
                                *_tpos = tpos;
@@ -222,7 +222,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                for (k = 0; k < b->core.n_cigar; ++k) {
                                        int op = cigar[k]&0xf;
                                        int j, l = cigar[k]>>4;
-                                       if (op == BAM_CMATCH) {
+                                       if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
                                                for (j = 0; j < l; ++j)
                                                        if (x + j >= left && x + j < right)
                                                                cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;