Update BIN values in 'samtools depad'

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index a8da562d0872e8b0930bb2bdd3dcc9abb58bab7b..476e393166983b0d00434789ad8596f0403a8f34 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -195,6 +195,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
                        replace_cigar(b, n2, cigar2);
                        posmap = update_posmap(posmap, r);
+                       b->core.bin = bam_reg2bin(0, bam_calend(&b->core, bam1_cigar(b)));
                } else if (b->core.n_cigar > 0) {
                        int i, k, op;
                        if (b->core.tid < 0) {
@@ -272,6 +273,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        n2 = k;
                        replace_cigar(b, n2, cigar2);
                        b->core.pos = posmap[b->core.pos];
+                       b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core.pos, bam1_cigar(b)));
                        if (b->core.mtid < 0 || b->core.mpos < 0) {
                                /* Nice case, no mate to worry about*/
                                // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));