X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_import.c;h=427140db9cbe9e3c80d173b0d69e31b1774c3037;hb=d0e30eec1158752010659982342a611fc91ae8e3;hp=9daa29f42a1676077b29f3f63ab7a7027896dbad;hpb=f1222861f3824c28d35cd143f5565ca09d80f056;p=samtools.git

diff --git a/bam_import.c b/bam_import.c
index 9daa29f..427140d 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -5,7 +5,12 @@
 #include <stdlib.h>
 #include <unistd.h>
 #include <assert.h>
+#ifdef _WIN32
+#include <fcntl.h>
+#endif
+#include "kstring.h"
 #include "bam.h"
+#include "sam_header.h"
 #include "kseq.h"
 #include "khash.h"
 
@@ -35,6 +40,25 @@ unsigned char bam_nt16_table[256] = {
 	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
 };
 
+unsigned short bam_char2flag_table[256] = {
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+	BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
 
 struct __tamFile_t {
@@ -42,6 +66,7 @@ struct __tamFile_t {
 	kstream_t *ks;
 	kstring_t *str;
 	uint64_t n_lines;
+	int is_first;
 };
 
 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
@@ -97,9 +122,10 @@ bam_header_t *sam_header_read2(const char *fn)
 	kstring_t *str;
 	kh_ref_t *hash;
 	khiter_t k;
-	hash = kh_init(ref);
+	if (fn == 0) return 0;
 	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
-	assert(fp);
+	if (fp == 0) return 0;
+	hash = kh_init(ref);
 	ks = ks_init(fp);
 	str = (kstring_t*)calloc(1, sizeof(kstring_t));
 	while (ks_getuntil(ks, 0, str, &dret) > 0) {
@@ -144,28 +170,76 @@ 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, z = 0;
-	bam1_core_t *c = &b->core;
-	kstring_t *str = fp->str;
-	kstream_t *ks = fp->ks;
+	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+	if (h->rg2lib) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
+	return sam_tbl_size(h->rg2lib);
+}
 
+int sam_header_parse(bam_header_t *h)
+{
+	void *tbl;
+	char **tmp;
+	int i;
+	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;
+	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+	tbl = sam_header2tbl(h->dict, "SQ", "SN", "LN");
+	h->n_targets = sam_tbl_size(tbl);
+	if (h->n_targets == 0) {
+		sam_tbl_destroy(tbl);
+		return 0;
+	}
+	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
+	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
+	tmp = (char**)calloc(h->n_targets, sizeof(void*));
+	sam_tbl_pair(tbl, h->target_name, tmp);
+	for (i = 0; i < h->n_targets; ++i)
+		h->target_len[i] = atoi(tmp[i]);
+	free(tmp);
+	sam_tbl_destroy(tbl);
+	return h->n_targets;
+}
+
+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
-		z += str->l + 1;
 		str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 		append_text(header, str);
 		if (dret != '\n') {
 			ret = ks_getuntil(fp->ks, '\n', str, &dret);
-			z += str->l + 1;
 			str->s[str->l] = '\n'; // NOT null terminated!!
 			append_text(header, str);
 		}
 		++fp->n_lines;
 	}
-	while (ret == 0) { // special consideration for "\r\n" and empty lines
-		ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
-		if (ret >= 0) z += str->l + 1;
+	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;
@@ -176,9 +250,26 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 		doff += c->l_qname;
 	}
-	{ // flag, tid, pos, qual
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+	{ // flag
+		long flag;
+		char *s;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		flag = strtol((char*)str->s, &s, 0);
+		if (*s) { // not the end of the string
+			flag = 0;
+			for (s = str->s; *s; ++s)
+				flag |= bam_char2flag_table[(int)*s];
+		}
+		c->flag = flag;
+	}
+	{ // tid, pos, qual
 		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;
@@ -199,7 +290,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 				x = strtol(s, &t, 10);
 				op = toupper(*t);
-				if (op == 'M') op = BAM_CMATCH;
+				if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
 				else if (op == 'I') op = BAM_CINS;
 				else if (op == 'D') op = BAM_CDEL;
 				else if (op == 'N') op = BAM_CREF_SKIP;
@@ -213,7 +304,13 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 			doff += c->n_cigar * 4;
-		} else c->bin = bam_reg2bin(c->pos, c->pos + 1);
+		} else {
+			if (!(c->flag&BAM_FUNMAP)) {
+				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+				c->flag |= BAM_FUNMAP;
+			}
+			c->bin = bam_reg2bin(c->pos, c->pos + 1);
+		}
 	}
 	{ // mtid, mpos, isize
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
@@ -226,16 +323,18 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 	}
 	{ // seq and qual
 		int i;
-		uint8_t *p;
+		uint8_t *p = 0;
 		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");
-		p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
-		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 (strcmp(str->s, "*")) {
+			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");
+			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+			memset(p, 0, (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);
+		} else c->l_qseq = 0;
 		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))
@@ -331,11 +430,12 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 tamFile sam_open(const char *fn)
 {
 	tamFile fp;
+	gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
+	if (gzfp == 0) return 0;
 	fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+	fp->fp = gzfp;
 	fp->ks = ks_init(fp->fp);
-	fp->n_lines = 0;
 	return fp;
 }