* samtools-0.1.4-22 (r369)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index d18716ff72164ea9d8c9ad63efad9e1b308a28f2..5d5506fb5630a088f692e6f0c64e8b827f6a5329 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -17,6 +17,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t)
 #define BAM_PLF_INDEL_ONLY 0x04
 #define BAM_PLF_GLF        0x08
 #define BAM_PLF_VAR_ONLY   0x10
+#define BAM_PLF_2ND        0x20
 
 typedef struct {
        bam_header_t *h;
@@ -248,6 +249,21 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                if (c > 126) c = 126;
                putchar(c);
        }
+       if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities
+               const unsigned char *q;
+               putchar('\t');
+               for (i = 0; i < n; ++i) {
+                       const bam_pileup1_t *p = pu + i;
+                       q = bam_aux_get(p->b, "E2");
+                       putchar(q? q[p->qpos + 1] : 'N');
+               }
+               putchar('\t');
+               for (i = 0; i < n; ++i) {
+                       const bam_pileup1_t *p = pu + i;
+                       q = bam_aux_get(p->b, "U2");
+                       putchar(q? q[p->qpos + 1] : '!');
+               }
+       }
        // print mapping quality if -s is flagged on the command line
        if (d->format & BAM_PLF_SIMPLE) {
                putchar('\t');
@@ -282,7 +298,7 @@ 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:S")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2")) >= 0) {
                switch (c) {
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
@@ -297,6 +313,7 @@ int bam_pileup(int argc, char *argv[])
                case 'v': d->format |= BAM_PLF_VAR_ONLY; break;
                case 'm': d->mask = strtol(optarg, 0, 0); break;
                case 'g': d->format |= BAM_PLF_GLF; break;
+               case '2': d->format |= BAM_PLF_2ND; break;
                case 'I': d->ido->q_indel = atoi(optarg); break;
                case 'G': d->ido->r_indel = atof(optarg); break;
                case 'S': is_SAM = 1; break;
@@ -309,6 +326,7 @@ 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, "        -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);