Imported Upstream version 0.1.6~dfsg

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5d5506fb5630a088f692e6f0c64e8b827f6a5329..5bf1ed095096b7cd91fc99d2256467b89e394d33 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -284,7 +284,8 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                printf("%d\t%d\t", rms_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", rms_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);
+               printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
+               printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);

                bam_maqindel_ret_destroy(r);
        }
        return 0;
                bam_maqindel_ret_destroy(r);
        }
        return 0;


@@ -330,7 +331,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);

-               fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
+               fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");

                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");


@@ -356,6 +357,8 @@ int bam_pileup(int argc, char *argv[])
        }
        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
        }
        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");

+       if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
+

        {
                samfile_t *fp;
                fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
        {
                samfile_t *fp;
                fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);