Release samtools-0.1.4

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 7bc422f508b36e13cc2a0405ac11c986357349f6..1d5ea5a82da2076217deb9bf224a5ed12b0655ef 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -151,7 +151,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 {
        pu_data_t *d = (pu_data_t*)data;
        bam_maqindel_ret_t *r = 0;
-       int i, j, rb, max_mapq = 0, *proposed_indels = 0;
+       int i, j, rb, rms_mapq = -1, max_mapq = 0, *proposed_indels = 0;
        uint32_t x;
 
        if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data);
@@ -181,6 +181,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                        if (ref_q > 255) ref_q = 255;
                }
                printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff);
+               rms_mapq = x>>16&0xff;
        }
        if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) {
                if (proposed_indels)
@@ -235,7 +236,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]);
                else printf("%s/%s\t", r->s[0], r->s[1]);
                printf("%d\t%d\t", r->q_cns, r->q_ref);
-               printf("%d\t%d\t", max_mapq, n);
+               printf("%d\t%d\t", rms_mapq >= 0? rms_mapq : max_mapq, n);
                printf("%s\t%s\t", r->s[0], r->s[1]);
                //printf("%d\t%d\t", r->gl[0], r->gl[1]);
                printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);