added a hidden option in pileup to output the base position (for Erin)

diff --git a/bam_plcmd.c b/bam_plcmd.c
index f8ae6b451f2f1d1da9a2b17d6c7085f4f5f2600c..ccaa28dec1dffc5174d77c31dc81603f8214b38c 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -21,6 +21,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t)
 #define BAM_PLF_RANBASE    0x40
 #define BAM_PLF_1STBASE    0x80
 #define BAM_PLF_ALLBASE    0x100
+#define BAM_PLF_READPOS    0x200
 
 typedef struct {
        bam_header_t *h;
@@ -299,6 +300,15 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                        putchar(c);
                }
        }
+       // print read position
+       if (d->format & BAM_PLF_READPOS) {
+               putchar('\t');
+               for (i = 0; i < n; ++i) {
+                       int x = pu[i].qpos;
+                       int l = pu[i].b->core.l_qseq;
+                       printf("%d,", x < l/2? x+1 : -((l-1)-x+1));
+               }
+       }
        putchar('\n');
        // print the indel line if r has been calculated. This only happens if:
        // a) -c or -i are flagged, AND b) the reference sequence is available
@@ -326,7 +336,7 @@ 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:d:im:gI:G:vM:S2aR:")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:P")) >= 0) {
                switch (c) {
                case 'a': d->c->is_soap = 1; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
@@ -344,6 +354,7 @@ int bam_pileup(int argc, char *argv[])
                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 'P': d->format |= BAM_PLF_READPOS; 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;