X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_import.c;h=fccaa022208131b27093a2b44f32e74d13a469c0;hb=3ddb3942053df00fdae714e77cbc2f5618db617e;hp=7742d2fbe2c17eacdcc131bcda256a93618e8d01;hpb=ecbde30918d2dc8ed3fcbad5e4cff44d0977dc34;p=samtools.git

diff --git a/bam_import.c b/bam_import.c
index 7742d2f..fccaa02 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -5,6 +5,7 @@
 #include <stdlib.h>
 #include <unistd.h>
 #include <assert.h>
+#include "kstring.h"
 #include "bam.h"
 #include "kseq.h"
 #include "khash.h"
@@ -42,31 +43,30 @@ struct __tamFile_t {
 	kstream_t *ks;
 	kstring_t *str;
 	uint64_t n_lines;
+	int is_first;
 };
 
-char **bam_load_pos(const char *fn, int *_n)
+char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
 {
 	char **list = 0, *s;
-	int n = 0, dret, m = 0, c;
+	int n = 0, dret, m = 0;
 	gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 	kstream_t *ks;
 	kstring_t *str;
 	str = (kstring_t*)calloc(1, sizeof(kstring_t));
 	ks = ks_init(fp);
-	while (ks_getuntil(ks, 0, str, &dret) > 0) {
+	while (ks_getuntil(ks, '\n', str, &dret) > 0) {
 		if (n == m) {
 			m = m? m << 1 : 16;
 			list = (char**)realloc(list, m * sizeof(char*));
 		}
-		s = list[n++] = (char*)calloc(str->l + 5, 1);
+		if (str->s[str->l-1] == '\r')
+			str->s[--str->l] = '\0';
+		s = list[n++] = (char*)calloc(str->l + 1, 1);
 		strcpy(s, str->s);
-		s += str->l + 1;
-		ks_getuntil(ks, 0, str, &dret);
-		*((uint32_t*)s) = atoi(str->s);
-		if (dret != '\n')
-			while ((c = ks_getc(fp)) >= 0 && c != '\n');
 	}
 	ks_destroy(ks);
+	gzclose(fp);
 	free(str->s); free(str);
 	*_n = n;
 	return list;
@@ -104,7 +104,7 @@ bam_header_t *sam_header_read2(const char *fn)
 	assert(fp);
 	ks = ks_init(fp);
 	str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+	while (ks_getuntil(ks, 0, str, &dret) > 0) {
 		char *s = strdup(str->s);
 		int len, i;
 		i = kh_size(hash);
@@ -146,14 +146,116 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
 	header->l_text += str->l + 1;
 	header->text[header->l_text] = 0;
 }
-int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+
+int sam_header_parse_rg(bam_header_t *h)
 {
-	int ret, doff, doff0, dret;
-	bam1_core_t *c = &b->core;
-	kstring_t *str = fp->str;
-	kstream_t *ks = fp->ks;
+	kstring_t *rgid, *rglib;
+	char *p, *q, *s, *r;
+	int n = 0;
+
+	// free
+	if (h == 0) return 0;
+	bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
+	if (h->l_text < 3) return 0;
+	// parse @RG lines
+	h->rg2lib = bam_strmap_init();
+	rgid = calloc(1, sizeof(kstring_t));
+	rglib = calloc(1, sizeof(kstring_t));
+	s = h->text;
+	while ((s = strstr(s, "@RG")) != 0) {
+		if (rgid->l && rglib->l) {
+			bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+			++n;
+		}
+		rgid->l = rglib->l = 0;
+		s += 3;
+		r = s;
+		if ((p = strstr(s, "ID:")) != 0) {
+			q = p + 3;
+			for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+			kputsn(q, p - q, rgid);
+		} else {
+			fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
+			break;
+		}
+		if (r < p) r = p;
+		if ((p = strstr(s, "LB:")) != 0) {
+			q = p + 3;
+			for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+			kputsn(q, p - q, rglib);
+		} else {
+			fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
+			break;
+		}
+		if (r < p) r = p;
+		s = r + 3;
+	}
+	if (rgid->l && rglib->l) {
+		bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+		++n;
+	}
+	free(rgid->s); free(rgid);
+	free(rglib->s); free(rglib);
+	if (n == 0) {
+		bam_strmap_destroy(h->rg2lib);
+		h->rg2lib = 0;
+	}
+	return n;
+}
+
+int sam_header_parse(bam_header_t *h)
+{
+	int i;
+	char *s, *p, *q, *r;
+
+	// free
+	free(h->target_len); free(h->target_name);
+	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
+	if (h->l_text < 3) return 0;
+	// count number of @SQ
+	s = h->text;
+	while ((s = strstr(s, "@SQ")) != 0) {
+		++h->n_targets;
+		s += 3;
+	}
+	if (h->n_targets == 0) return 0;
+	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
+	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
+	// parse @SQ lines
+	i = 0;
+	s = h->text;
+	while ((s = strstr(s, "@SQ")) != 0) {
+		s += 3;
+		r = s;
+		if ((p = strstr(s, "SN:")) != 0) {
+			q = p + 3;
+			for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+			h->target_name[i] = (char*)calloc(p - q + 1, 1);
+			strncpy(h->target_name[i], q, p - q);
+		} else goto header_err_ret;
+		if (r < p) r = p;
+		if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
+		else goto header_err_ret;
+		if (r < p) r = p;
+		s = r + 3;
+		++i;
+	}
+	sam_header_parse_rg(h);
+	return h->n_targets;
 
-	while ((ret = ks_getuntil(fp->ks, 0, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+header_err_ret:
+	fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
+	free(h->target_len); free(h->target_name);
+	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
+	return 0;
+}
+
+bam_header_t *sam_header_read(tamFile fp)
+{
+	int ret, dret;
+	bam_header_t *header = bam_header_init();
+	kstring_t *str = fp->str;
+	while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 		str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 		append_text(header, str);
 		if (dret != '\n') {
@@ -163,7 +265,28 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		}
 		++fp->n_lines;
 	}
-	while (ret == 0) ret = ks_getuntil(fp->ks, 0, str, &dret); // special consideration for "\r\n"
+	sam_header_parse(header);
+	bam_init_header_hash(header);
+	fp->is_first = 1;
+	return header;
+}
+
+int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+{
+	int ret, doff, doff0, dret, z = 0;
+	bam1_core_t *c = &b->core;
+	kstring_t *str = fp->str;
+	kstream_t *ks = fp->ks;
+
+	if (fp->is_first) {
+		fp->is_first = 0;
+		ret = str->l;
+	} else {
+		do { // special consideration for empty lines
+			ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
+			if (ret >= 0) z += str->l + 1;
+		} while (ret == 0);
+	}
 	if (ret < 0) return -1;
 	++fp->n_lines;
 	doff = 0;
@@ -174,10 +297,16 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		doff += c->l_qname;
 	}
 	{ // flag, tid, pos, qual
-		ret = ks_getuntil(ks, 0, str, &dret); c->flag = atoi(str->s);
-		ret = ks_getuntil(ks, 0, str, &dret); c->tid = bam_get_tid(header, str->s);
-		ret = ks_getuntil(ks, 0, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-		ret = ks_getuntil(ks, 0, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
+		if (c->tid < 0 && strcmp(str->s, "*")) {
+			if (header->n_targets == 0) {
+				fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+				exit(1);
+			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+		}
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 		if (ret < 0) return -2;
 	}
 	{ // cigar
@@ -185,7 +314,8 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		int i, op;
 		long x;
 		c->n_cigar = 0;
-		if (ks_getuntil(ks, 0, str, &dret) < 0) return -3;
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
+		z += str->l + 1;
 		if (str->s[0] != '*') {
 			for (s = str->s; *s; ++s) {
 				if (isalpha(*s)) ++c->n_cigar;
@@ -212,15 +342,19 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		} else c->bin = bam_reg2bin(c->pos, c->pos + 1);
 	}
 	{ // mtid, mpos, isize
-		ret = ks_getuntil(ks, 0, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
-		ret = ks_getuntil(ks, 0, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-		ret = ks_getuntil(ks, 0, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 		if (ret < 0) return -4;
 	}
 	{ // seq and qual
 		int i;
 		uint8_t *p;
-		if (ks_getuntil(ks, 0, str, &dret) < 0) return -5; // seq
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
+		z += str->l + 1;
 		c->l_qseq = strlen(str->s);
 		if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 			parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
@@ -228,17 +362,20 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		bzero(p, (c->l_qseq+1)/2);
 		for (i = 0; i < c->l_qseq; ++i)
 			p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
-		if (ks_getuntil(ks, 0, str, &dret) < 0) return -6; // qual
-		if (c->l_qseq != strlen(str->s))
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
+		z += str->l + 1;
+		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 			parse_error(fp->n_lines, "sequence and quality are inconsistent");
 		p += (c->l_qseq+1)/2;
-		for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+		if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+		else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 		doff += c->l_qseq + (c->l_qseq+1)/2;
 	}
 	doff0 = doff;
 	if (dret != '\n' && dret != '\r') { // aux
-		while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+		while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 			uint8_t *s, type, key[2];
+			z += str->l + 1;
 			if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 				parse_error(fp->n_lines, "missing colon in auxiliary data");
 			key[0] = str->s[0]; key[1] = str->s[1];
@@ -287,6 +424,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 				*s++ = 'f';
 				*(float*)s = (float)atof(str->s + 5);
 				s += 4; doff += 5;
+			} else if (type == 'd') {
+				s = alloc_data(b, doff + 9) + doff;
+				*s++ = 'd';
+				*(float*)s = (float)atof(str->s + 9);
+				s += 8; doff += 9;
 			} else if (type == 'Z' || type == 'H') {
 				int size = 1 + (str->l - 5) + 1;
 				if (type == 'H') { // check whether the hex string is valid
@@ -309,7 +451,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 	}
 	b->l_aux = doff - doff0;
 	b->data_len = doff;
-	return 0;
+	return z;
 }
 
 tamFile sam_open(const char *fn)
@@ -319,7 +461,6 @@ tamFile sam_open(const char *fn)
 	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 	fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 	fp->ks = ks_init(fp->fp);
-	fp->n_lines = 0;
 	return fp;
 }
 
@@ -332,41 +473,3 @@ void sam_close(tamFile fp)
 		free(fp);
 	}
 }
-
-static void taf2baf_core(const char *fntaf, const char *fnbaf, bam_header_t *header)
-{
-	bamFile fpbaf;
-	bam1_t *b;
-	tamFile fp;
-	int ret;
-
-	b = (bam1_t*)calloc(1, sizeof(bam1_t));
-	fpbaf = (strcmp(fnbaf, "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(fnbaf, "w");
-	fp = sam_open(fntaf);
-	ret = sam_read1(fp, header, b);
-	bam_header_write(fpbaf, header);
-	if (ret >= 0) {
-		bam_write1(fpbaf, b);
-		while (sam_read1(fp, header, b) >= 0) bam_write1(fpbaf, b);
-	}
-	bam_close(fpbaf);
-	free(b->data); free(b);
-	sam_close(fp);
-}
-
-int bam_taf2baf(int argc, char *argv[])
-{
-	int c;
-	bam_header_t *header;
-
-	while ((c = getopt(argc, argv, "")) >= 0) {
-	}
-	if (optind + 3 > argc) {
-		fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
-		return 1;
-	}
-	header = sam_header_read2(argv[optind]);
-	taf2baf_core(argv[optind+1], argv[optind+2], header);
-	bam_header_destroy(header);
-	return 0;
-}