X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=b1ffdf900cfa7212937b54ead357bbd3bb8579a0;hb=63e4e54189bc9e7f43852edf865f95e713b93dc4;hp=2fe32b4909bc2fe2b9f26c143b213382c8641fe9;hpb=ecbde30918d2dc8ed3fcbad5e4cff44d0977dc34;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2fe32b4..b1ffdf9 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -6,7 +6,10 @@
 #include "bam_maqcns.h"
 #include "khash.h"
 #include "glf.h"
-KHASH_SET_INIT_INT64(64)
+#include "kstring.h"
+
+typedef int *indel_list_t;
+KHASH_MAP_INIT_INT64(64, indel_list_t)
 
 #define BAM_PLF_SIMPLE     0x01
 #define BAM_PLF_CNS        0x02
@@ -26,83 +29,121 @@ typedef struct {
 	glfFile fp; // for glf output only
 } pu_data_t;
 
-char **bam_load_pos(const char *fn, int *_n);
+char **__bam_get_lines(const char *fn, int *_n);
 void bam_init_header_hash(bam_header_t *header);
 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
 
 static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
 {
-	int n, tmp, i;
-	char **list, *s;
-	uint64_t x;
+	char **list;
+	int i, j, n, *fields, max_fields;
 	khash_t(64) *hash;
 	bam_init_header_hash(h);
-	list = bam_load_pos(fn, &n);
+	list = __bam_get_lines(fn, &n);
 	hash = kh_init(64);
+	max_fields = 0; fields = 0;
 	for (i = 0; i < n; ++i) {
-		x = (uint64_t)bam_get_tid(h, list[i]) << 32;
-		s = list[i];
-		while (*s++);
-		x |= *((uint32_t*)s) - 1;
-		kh_put(64, hash, x, &tmp);
-		free(list[i]);
+		char *str = list[i];
+		int chr, n_fields, ret;
+		khint_t k;
+		uint64_t x;
+		n_fields = ksplit_core(str, 0, &max_fields, &fields);
+		if (n_fields < 2) continue;
+		chr = bam_get_tid(h, str + fields[0]);
+		if (chr < 0) {
+			fprintf(stderr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]);
+			continue;
+		}
+		x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1);
+		k = kh_put(64, hash, x, &ret);
+		if (ret == 0) {
+			fprintf(stderr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]);
+			continue;
+		}
+		kh_val(hash, k) = 0;
+		if (n_fields > 2) {
+			// count
+			for (j = 2; j < n_fields; ++j) {
+				char *s = str + fields[j];
+				if ((*s != '+' && *s != '-') || !isdigit(s[1])) break;
+ 			}
+			if (j > 2) { // update kh_val()
+				int *q, y, z;
+				q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int));
+				q[0] = j - 2; z = j; y = 1;
+				for (j = 2; j < z; ++j)
+					q[y++] = atoi(str + fields[j]);
+			}
+		}
+		free(str);
 	}
-	free(list);
+	free(list); free(fields);
 	return hash;
 }
 
 // an analogy to pileup_func() below
-static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
+static int glt3_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 rb;
+	int rb, *proposed_indels = 0;
 	glf1_t *g;
-	glf3_t g2;
+	glf3_t *g3;
+
 	if (d->fai == 0) {
-		fprintf(stderr, "[glt_func] reference sequence is required for generating GLT. Abort!\n");
+		fprintf(stderr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n");
 		exit(1);
 	}
-	if (d->hash && kh_get(64, d->hash, (uint64_t)tid<<32|pos) == kh_end(d->hash)) return 0;
+	if (d->hash) { // only output a list of sites
+		khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
+		if (k == kh_end(d->hash)) return 0;
+		proposed_indels = kh_val(d->hash, k);
+	}
+	g3 = glf3_init1();
 	if (d->fai && (int)tid != d->tid) {
 		if (d->ref) { // then write the end mark
-			memset(&g2, 0, sizeof(glf3_t));
-			g2.type = GLF_TYPE_END;
-			bgzf_write(d->fp, &g2, sizeof(glf3_t));
+			g3->rtype = GLF3_RTYPE_END;
+			glf3_write1(d->fp, g3);
 		}
-		glf_ref_write(d->fp, d->h->target_name[tid]); // write reference
+		glf3_ref_write(d->fp, d->h->target_name[tid], d->h->target_len[tid]); // write reference
 		free(d->ref);
 		d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
 		d->tid = tid;
+		d->last_pos = 0;
 	}
 	rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
 	g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
-	memcpy(&g2, g, sizeof(glf1_t));
-	g2.type = GLF_TYPE_NORMAL;
-	g2.offset = pos - d->last_pos;
+	memcpy(g3, g, sizeof(glf1_t));
+	g3->rtype = GLF3_RTYPE_SUB;
+	g3->offset = pos - d->last_pos;
 	d->last_pos = pos;
-	bgzf_write(d->fp, &g2, sizeof(glf3_t));
-	r = bam_maqindel(n, pos, d->ido, pu, d->ref);
+	glf3_write1(d->fp, 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 (r) { // then write indel line
-		int g3 = 3 * n, min;
-		min = g3;
+		int het = 3 * n, min;
+		min = het;
 		if (min > r->gl[0]) min = r->gl[0];
 		if (min > r->gl[1]) min = r->gl[1];
-		g2.ref_base = 0;
-		g2.type = GLF_TYPE_INDEL;
-		memset(g2.lk, 0, 10);
-		g2.lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
-		g2.lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
-		g2.lk[2] = g3 - min < 255? g3 - min : 255;
-		*(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
-		*(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
-		g2.min_lk = min < 255? min : 255;
-		bgzf_write(d->fp, &g2, sizeof(glf3_t));
-		if (r->indel1) bgzf_write(d->fp, r->s[0]+1, r->indel1>0? r->indel1 : -r->indel1);
-		if (r->indel2) bgzf_write(d->fp, r->s[1]+1, r->indel2>0? r->indel2 : -r->indel2);
+		g3->ref_base = 0;
+		g3->rtype = GLF3_RTYPE_INDEL;
+		memset(g3->lk, 0, 10);
+		g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
+		g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
+		g3->lk[2] = het - min < 255? het - min : 255;
+		g3->offset = 0;
+		g3->indel_len[0] = r->indel1;
+		g3->indel_len[1] = r->indel2;
+		g3->min_lk = min < 255? min : 255;
+		g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
+		g3->indel_seq[0] = strdup(r->s[0]+1);
+		g3->indel_seq[1] = strdup(r->s[1]+1);
+		glf3_write1(d->fp, g3);
 		bam_maqindel_ret_destroy(r);
 	}
 	free(g);
+	glf3_destroy1(g3);
 	return 0;
 }
 
@@ -110,11 +151,16 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 {
 	pu_data_t *d = (pu_data_t*)data;
 	bam_maqindel_ret_t *r = 0;
-	int i, j, rb, max_mapq = 0;
+	int i, j, rb, max_mapq = 0, *proposed_indels = 0;
 	uint32_t x;
-	if (d->hash && kh_get(64, d->hash, (uint64_t)tid<<32|pos) == kh_end(d->hash)) return 0;
-	if (d->format & BAM_PLF_GLF) return glt_func(tid, pos, n, pu, data);
-	if (d->fai && (int)tid != d->tid) {
+
+	if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data);
+	if (d->hash) { // only output a list of sites
+		khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
+		if (k == kh_end(d->hash)) return 0;
+		proposed_indels = kh_val(d->hash, k);
+	}
+	if (d->fai && (int)tid != d->tid) { // then update d->ref
 		free(d->ref);
 		d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
 		d->tid = tid;
@@ -136,9 +182,10 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		}
 		printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff);
 	}
-	if (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) {
-		if (d->ref) // indel calling
-			r = bam_maqindel(n, pos, d->ido, pu, d->ref);
+	if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) {
+		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);
 	}
 	// pileup strings
 	printf("%d\t", n);
@@ -148,8 +195,8 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		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 (toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-			else bam1_strand(p->b)? tolower(c) : toupper(c);
+			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);
@@ -191,7 +238,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		printf("%d\t%d\t", max_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\t%d\n", r->cnt1, r->cnt2, r->cnt_ambi, r->cnt_anti);
+		printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
 		bam_maqindel_ret_destroy(r);
 	}
 	return 0;
@@ -213,7 +260,7 @@ int bam_pileup(int argc, char *argv[])
 		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 = atoi(optarg); break;
+		case 'r': d->c->het_rate = atof(optarg); break;
 		case 'c': d->format |= BAM_PLF_CNS; break;
 		case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
 		case 'm': d->mask = atoi(optarg); break;
@@ -225,7 +272,7 @@ int bam_pileup(int argc, char *argv[])
 	}
 	if (optind == argc) {
 		fprintf(stderr, "\n");
-		fprintf(stderr, "Usage:  bamtk pileup [options] <in.bam>|<in.sam>\n\n");
+		fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
 		fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\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);
@@ -233,7 +280,7 @@ int bam_pileup(int argc, char *argv[])
 		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, "        -g        output in the extended GLT format (suppressing -c/-i/-s)\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);
 		fprintf(stderr, "        -N INT    number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
 		fprintf(stderr, "        -r FLOAT  prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
@@ -245,15 +292,17 @@ int bam_pileup(int argc, char *argv[])
 	}
 	if (fn_fa) d->fai = fai_load(fn_fa);
 	free(fn_fa);
-	bam_maqcns_prepare(d->c);
+	if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c);
 	if (d->format & BAM_PLF_GLF) {
-		glf_header_t *h;
-		h = glf_header_init();
+		glf3_header_t *h;
+		h = glf3_header_init();
 		d->fp = bgzf_fdopen(fileno(stdout), "w");
-		glf_header_write(d->fp, h);
-		glf_header_destroy(h);
+		glf3_header_write(d->fp, h);
+		glf3_header_destroy(h);
 	}
-	if (fn_list) {
+	if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
+		fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
+	if (fn_list) { // the input is SAM
 		tamFile fp;
 		bam1_t *b;
 		int ret;
@@ -269,17 +318,26 @@ int bam_pileup(int argc, char *argv[])
 		bam_plbuf_destroy(buf);
 		bam_destroy1(b);
 		sam_close(fp);
-	} else {
+	} else { // the input is BAM
 		bamFile fp;
 		fp = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
 		d->h = bam_header_read(fp);
+		if (d->h == 0) {
+			fprintf(stderr, "[bam_pileup] fail to read the BAM header. Abort!\n");
+			return 1;
+		}
 		if (fn_pos) d->hash = load_pos(fn_pos, d->h);
 		bam_pileup_file(fp, d->mask, pileup_func, d);
 		bam_close(fp);
 	}
 	if (d->format & BAM_PLF_GLF) bgzf_close(d->fp);
+	if (fn_pos) { // free the hash table
+		khint_t k;
+		for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
+			if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
+		kh_destroy(64, d->hash);
+	}
 	free(fn_pos); free(fn_list);
-	kh_destroy(64, d->hash);
 	bam_header_destroy(d->h);
 	if (d->fai) fai_destroy(d->fai);
 	bam_maqcns_destroy(d->c);