Merge commit 'upstream/0.1.7a.dfsg'

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5d5506fb5630a088f692e6f0c64e8b827f6a5329..ba787a98bd78726503f48af1fd16582d89a357dd 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -121,9 +121,11 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
        g3->offset = pos - d->last_pos;
        d->last_pos = pos;
        glf3_write1(d->fp_glf, g3);
-       if (proposed_indels)
-               r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-       else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+       if (pos < d->len) {
+               if (proposed_indels)
+                       r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+               else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+       }
        if (r) { // then write indel line
                int het = 3 * n, min;
                min = het;
@@ -182,7 +184,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        // call the consensus and indel
        if (d->format & BAM_PLF_CNS) // call consensus
                cns = bam_maqcns_call(n, pu, d->c);
-       if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // call indels
+       if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
                if (proposed_indels) // the first element gives the size of the array
                        r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
                else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
@@ -284,7 +286,8 @@ 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%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;
@@ -298,8 +301,9 @@ int bam_pileup(int argc, char *argv[])
        d->tid = -1; d->mask = BAM_DEF_MASK;
        d->c = bam_maqcns_init();
        d->ido = bam_maqindel_opt_init();
-       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2a")) >= 0) {
                switch (c) {
+               case 'a': d->c->is_soap = 1; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
                case 'l': fn_pos = strdup(optarg); break;
@@ -326,11 +330,12 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
                fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
                fprintf(stderr, "        -S        the input is in SAM\n");
+               fprintf(stderr, "        -a        use the SOAPsnp model for SNP calling\n");
                fprintf(stderr, "        -2        output the 2nd best call and quality\n");
                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");
@@ -356,6 +361,8 @@ 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 (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);