* samtools-0.1.7-5 (r528)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 391767ab134833f5dcc5ea914866fd7f10b97718..cbb55cc3a5a7d1643b729c63bd1c36ad206e6387 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -18,6 +18,9 @@ KHASH_MAP_INIT_INT64(64, indel_list_t)
 #define BAM_PLF_GLF        0x08
 #define BAM_PLF_VAR_ONLY   0x10
 #define BAM_PLF_2ND        0x20
+#define BAM_PLF_RANBASE    0x40
+#define BAM_PLF_1STBASE    0x80
+#define BAM_PLF_ALLBASE    0x100
 
 typedef struct {
        bam_header_t *h;
@@ -121,9 +124,11 @@ 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;
@@ -180,9 +185,27 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                if (i == n) return 0;
        }
        // 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) { // call consensus
+               if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call
+                       const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n);
+                       int q = bam1_qual(p->b)[p->qpos];
+                       int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+                       uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos);
+                       cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8;
+               } else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases
+                       uint64_t rmsQ = 0;
+                       uint32_t b = 0;
+                       for (i = 0; i < n; ++i) {
+                               const bam_pileup1_t *p = pu + i;
+                               int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+                               b |= bam1_seqi(bam1_seq(p->b), p->qpos);
+                               rmsQ += q * q;
+                       }
+                       rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499);
+                       cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8;
+               } else cns = bam_maqcns_call(n, pu, d->c);
+       }
+       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 +307,8 @@ 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 +322,9 @@ 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:S2aR:")) >= 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;
@@ -317,6 +342,12 @@ int bam_pileup(int argc, char *argv[])
                case 'I': d->ido->q_indel = atoi(optarg); break;
                case 'G': d->ido->r_indel = atof(optarg); break;
                case 'S': is_SAM = 1; break;
+               case 'R':
+                       if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE;
+                       else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE;
+                       else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE;
+                       else fprintf(stderr, "[bam_pileup] unrecognized -R\n");
+                       break;
                default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
                }
        }
@@ -326,6 +357,7 @@ 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, "        -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);
@@ -345,6 +377,7 @@ int bam_pileup(int argc, char *argv[])
                free(fn_list); free(fn_fa); free(d);
                return 1;
        }
+       if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS;
        if (fn_fa) d->fai = fai_load(fn_fa);
        if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
        if (d->format & BAM_PLF_GLF) { // for glf output