X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=cbb55cc3a5a7d1643b729c63bd1c36ad206e6387;hb=6971381d1e639d69dd3d72f8f16e2726c95fd3e4;hp=5bf1ed095096b7cd91fc99d2256467b89e394d33;hpb=2ec779405b1f89e1407c24956bbb3af584234bc9;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5bf1ed0..cbb55cc 100644
--- 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);
@@ -299,8 +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;
@@ -318,6 +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;
 		}
 	}
@@ -327,6 +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);
@@ -346,6 +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