X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=6804795bd107405982cada8544051cc073fdf55e;hp=ba787a98bd78726503f48af1fd16582d89a357dd;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/bam_plcmd.c b/bam_plcmd.c
index ba787a9..6804795 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -18,6 +18,10 @@ 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
+#define BAM_PLF_READPOS    0x200
 
 typedef struct {
 	bam_header_t *h;
@@ -28,6 +32,7 @@ typedef struct {
 	uint32_t format;
 	int tid, len, last_pos;
 	int mask;
+    int max_depth;  // for indel calling, ignore reads with the depth too high. 0 for unlimited
 	char *ref;
 	glfFile fp_glf; // for glf output only
 } pu_data_t;
@@ -121,10 +126,11 @@ 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 (pos < d->len) {
+    if (pos < d->len) {
+        int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
 		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);
+			r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+		else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
 	}
 	if (r) { // then write indel line
 		int het = 3 * n, min;
@@ -152,11 +158,37 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
 	return 0;
 }
 
+static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+{
+	if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+	if (!p->is_del) {
+		int j, rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+		rb = (ref && pos < ref_len)? ref[pos] : 'N';
+		if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+		else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+		putchar(c);
+		if (p->indel > 0) {
+			printf("+%d", p->indel);
+			for (j = 1; j <= p->indel; ++j) {
+				c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+				putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+			}
+		} else if (p->indel < 0) {
+			printf("%d", p->indel);
+			for (j = 1; j <= -p->indel; ++j) {
+				c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+				putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+			}
+		}
+	} else putchar('*');
+	if (p->is_tail) putchar('$');
+}
+
 static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
 {
 	pu_data_t *d = (pu_data_t*)data;
 	bam_maqindel_ret_t *r = 0;
-	int i, j, rb, rms_mapq = -1, *proposed_indels = 0;
+	int i, rb, rms_mapq = -1, *proposed_indels = 0;
 	uint64_t rms_aux;
 	uint32_t cns = 0;
 
@@ -171,7 +203,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 	// update d->ref if necessary
 	if (d->fai && (int)tid != d->tid) {
 		free(d->ref);
-		d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
+		d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &d->len);
 		d->tid = tid;
 	}
 	rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
@@ -182,12 +214,31 @@ 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 && 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);
+	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
+        int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
+        if (proposed_indels) // the first element gives the size of the array
+            r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+        else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
 	}
 	// when only variant sites are asked for, test if the site is a variant
 	if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) {
@@ -218,27 +269,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		const bam_pileup1_t *p = pu + i;
 		int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
 		rms_aux += tmp * tmp;
-		if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
-		if (!p->is_del) {
-			int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-			if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
-			putchar(c);
-			if (p->indel > 0) {
-				printf("+%d", p->indel);
-				for (j = 1; j <= p->indel; ++j) {
-					c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
-					putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
-				}
-			} else if (p->indel < 0) {
-				printf("%d", p->indel);
-				for (j = 1; j <= -p->indel; ++j) {
-					c = (d->ref && (int)pos+j < d->len)? d->ref[pos+j] : 'N';
-					putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
-				}
-			}
-		} else putchar('*');
-		if (p->is_tail) putchar('$');
+		pileup_seq(p, pos, d->len, d->ref);
 	}
 	// finalize rms_mapq
 	rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
@@ -275,6 +306,15 @@ 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
@@ -298,29 +338,40 @@ int bam_pileup(int argc, char *argv[])
 	int c, is_SAM = 0;
 	char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
 	pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
+    d->max_depth = 0;
 	d->tid = -1; d->mask = BAM_DEF_MASK;
 	d->c = bam_maqcns_init();
+	d->c->is_soap = 1; // change the default model
 	d->ido = bam_maqindel_opt_init();
-	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2a")) >= 0) {
+	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PA")) >= 0) {
 		switch (c) {
 		case 'a': d->c->is_soap = 1; break;
+		case 'A': d->c->is_soap = 0; break;
 		case 's': d->format |= BAM_PLF_SIMPLE; break;
 		case 't': fn_list = strdup(optarg); break;
 		case 'l': fn_pos = strdup(optarg); break;
 		case 'f': fn_fa = strdup(optarg); break;
 		case 'T': d->c->theta = atof(optarg); break;
 		case 'N': d->c->n_hap = atoi(optarg); break;
-		case 'r': d->c->het_rate = atof(optarg); break;
+		case 'r': d->c->het_rate = atof(optarg); d->ido->r_snp = d->c->het_rate; break;
 		case 'M': d->c->cap_mapQ = atoi(optarg); break;
+		case 'd': d->max_depth = atoi(optarg); break;
 		case 'c': d->format |= BAM_PLF_CNS; break;
 		case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
 		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 '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;
+		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;
 		}
 	}
@@ -330,15 +381,16 @@ 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, "        -A        use the MAQ 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, "        -d INT    limit maximum depth for indels [unlimited]\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");
+		fprintf(stderr, "        -c        output the SOAPsnp consensus sequence\n");
 		fprintf(stderr, "        -v        print variants only (for -c)\n");
 		fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
 		fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
@@ -350,6 +402,7 @@ 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
@@ -390,3 +443,128 @@ int bam_pileup(int argc, char *argv[])
 	free(d->ido); free(d->ref); free(d);
 	return 0;
 }
+
+/***********
+ * mpileup *
+ ***********/
+
+typedef struct {
+	char *reg;
+	faidx_t *fai;
+} mplp_conf_t;
+
+typedef struct {
+	bamFile fp;
+	bam_iter_t iter;
+} mplp_aux_t;
+
+static int mplp_func(void *data, bam1_t *b)
+{
+	mplp_aux_t *ma = (mplp_aux_t*)data;
+	if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
+	return bam_read1(ma->fp, b);
+}
+
+static int mpileup(mplp_conf_t *conf, int n, char **fn)
+{
+	mplp_aux_t **data;
+	int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
+	const bam_pileup1_t **plp;
+	bam_mplp_t iter;
+	bam_header_t *h = 0;
+	char *ref;
+	// allocate
+	data = calloc(n, sizeof(void*));
+	plp = calloc(n, sizeof(void*));
+	n_plp = calloc(n, sizeof(int*));
+	// read the header and initialize data
+	for (i = 0; i < n; ++i) {
+		bam_header_t *h_tmp;
+		data[i] = calloc(1, sizeof(mplp_aux_t));
+		data[i]->fp = bam_open(fn[i], "r");
+		h_tmp = bam_header_read(data[i]->fp);
+		if (conf->reg) {
+			int beg, end;
+			bam_index_t *idx;
+			idx = bam_index_load(fn[i]);
+			if (idx == 0) {
+				fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
+				exit(1);
+			}
+			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
+				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
+				exit(1);
+			}
+			if (i == 0) beg0 = beg, end0 = end;
+			data[i]->iter = bam_iter_query(idx, tid, beg, end);
+			bam_index_destroy(idx);
+		}
+		if (i == 0) h = h_tmp;
+		else {
+			// FIXME: to check consistency
+			bam_header_destroy(h_tmp);
+		}
+	}
+	// mpileup
+	ref_tid = -1; ref = 0;
+	iter = bam_mplp_init(n, mplp_func, (void**)data);
+	while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
+		if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+		if (tid != ref_tid) {
+			free(ref);
+			if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+			ref_tid = tid;
+		}
+		printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+		for (i = 0; i < n; ++i) {
+			int j;
+			printf("\t%d\t", n_plp[i]);
+			if (n_plp[i] == 0) printf("*\t*");
+			else {
+				for (j = 0; j < n_plp[i]; ++j)
+					pileup_seq(plp[i] + j, pos, ref_len, ref);
+				putchar('\t');
+				for (j = 0; j < n_plp[i]; ++j) {
+					const bam_pileup1_t *p = plp[i] + j;
+					int c = bam1_qual(p->b)[p->qpos] + 33;
+					if (c > 126) c = 126;
+					putchar(c);
+				}
+			}
+		}
+		putchar('\n');
+	}
+	bam_mplp_destroy(iter);
+	bam_header_destroy(h);
+	for (i = 0; i < n; ++i) {
+		bam_close(data[i]->fp);
+		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+		free(data[i]);
+	}
+	free(data); free(plp); free(ref); free(n_plp);
+	return 0;
+}
+
+int bam_mpileup(int argc, char *argv[])
+{
+	int c;
+	mplp_conf_t mplp;
+	memset(&mplp, 0, sizeof(mplp_conf_t));
+	while ((c = getopt(argc, argv, "f:r:")) >= 0) {
+		switch (c) {
+		case 'f':
+			mplp.fai = fai_load(optarg);
+			if (mplp.fai == 0) return 1;
+			break;
+		case 'r': mplp.reg = strdup(optarg);
+		}
+	}
+	if (argc == 1) {
+		fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] in1.bam [in2.bam [...]]\n");
+		return 1;
+	}
+	mpileup(&mplp, argc - optind, argv + optind);
+	free(mplp.reg);
+	if (mplp.fai) fai_destroy(mplp.fai);
+	return 0;
+}