bugfix: wrong SP; missing DV in the VCF header

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 83f2e564b67b85c711b0a0b83d1e29fc52591eb5..6ac5dce182a2353ada163dd65bdb5ca530d59127 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -328,7 +328,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        if (bcr && fmt_flag) {
                uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0;
                uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0;
-               int32_t  *sp = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
+               int32_t  *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
                for (i = 0; i < bc->n; ++i) {
                        bcf_callret1_t *p = bcr + i;
                        if (dp) dp[i] = p->depth  < 0xffff? p->depth  : 0xffff;