X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=c665a923a8a2ec1eaab957444012689ffd8fab16;hb=8b0f98e2ac96b5ab07fd482cbaaa06d458254a90;hp=f8ae6b451f2f1d1da9a2b17d6c7085f4f5f2600c;hpb=7e56a1610a2f932ba2ef66b0e89b1170b9c654e1;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index f8ae6b4..c665a92 100644
--- 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;
@@ -157,11 +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;
 
@@ -242,27 +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);
@@ -299,6 +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
@@ -325,17 +341,19 @@ int bam_pileup(int argc, char *argv[])
     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:d:im:gI:G:vM:S2aR:")) >= 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;
@@ -344,6 +362,7 @@ 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;
@@ -362,7 +381,7 @@ 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, "        -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);
@@ -371,7 +390,7 @@ int bam_pileup(int argc, char *argv[])
 		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);
@@ -424,3 +443,143 @@ int bam_pileup(int argc, char *argv[])
 	free(d->ido); free(d->ref); free(d);
 	return 0;
 }
+
+/***********
+ * mpileup *
+ ***********/
+
+typedef struct {
+	char *reg, *fn_pos;
+	faidx_t *fai;
+	kh_64_t *hash;
+} 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;
+	khash_t(64) *hash = 0;
+	// 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);
+		}
+	}
+	if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
+	// 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 (hash) {
+			khint_t k;
+			k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
+			if (k == kh_end(hash)) continue;
+		}
+		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');
+	}
+	if (hash) { // free the hash table
+		khint_t k;
+		for (k = kh_begin(hash); k < kh_end(hash); ++k)
+			if (kh_exist(hash, k)) free(kh_val(hash, k));
+		kh_destroy(64, hash);
+	}
+	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:l:")) >= 0) {
+		switch (c) {
+		case 'f':
+			mplp.fai = fai_load(optarg);
+			if (mplp.fai == 0) return 1;
+			break;
+		case 'r': mplp.reg = strdup(optarg); break;
+		case 'l': mplp.fn_pos = strdup(optarg); break;
+		}
+	}
+	if (argc == 1) {
+		fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] 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;
+}