X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=fa11df6c12b1abc589415d4d11fe269067ecd765;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=a13327482614940078982ba3ec3ed2fd0d342647;hpb=f1222861f3824c28d35cd143f5565ca09d80f056;p=samtools.git

diff --git a/sam.c b/sam.c
index a133274..fa11df6 100644
--- a/sam.c
+++ b/sam.c
@@ -1,4 +1,6 @@
 #include <string.h>
+#include <unistd.h>
+#include "faidx.h"
 #include "sam.h"
 
 #define TYPE_BAM  1
@@ -10,7 +12,7 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 	int i;
 	h = bam_header_init();
 	*h = *h0;
-	h->hash = 0;
+	h->hash = h->dict = h->rg2lib = 0;
 	h->text = (char*)calloc(h->l_text + 1, 1);
 	memcpy(h->text, h0->text, h->l_text);
 	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
@@ -21,51 +23,23 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 	}
 	return h;
 }
-
-bam_header_t *bam_header_parse(const char *text)
+static void append_header_text(bam_header_t *header, char* text, int len)
 {
-	bam_header_t *h;
-	int i;
-	char *s, *p, *q, *r;
-
-	i = strlen(text);
-	if (i < 3) return 0; // headerless
-	h = bam_header_init();
-	h->l_text = i;
-	h->text = strdup(text);
-	s = h->text;
-	while ((s = strstr(s, "@SQ")) != 0) {
-		++h->n_targets;
-		s += 3;
-	}
-	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
-	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
-	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);
-			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;
-	}
-	if (h->n_targets == 0) {
-		bam_header_destroy(h);
-		return 0;
-	} else return h;
+	int x = header->l_text + 1;
+	int y = header->l_text + len + 1; // 1 byte null
+	if (text == 0) return;
+	kroundup32(x); 
+	kroundup32(y);
+	if (x < y) header->text = (char*)realloc(header->text, y);
+	strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
+	header->l_text += len;
+	header->text[header->l_text] = 0;
+}
 
-header_err_ret:
-	fprintf(stderr, "[bam_header_parse] missing SN tag in a @SQ line.\n");
-	bam_header_destroy(h);
+int samthreads(samfile_t *fp, int n_threads, int n_sub_blks)
+{
+	if (!(fp->type&1) || (fp->type&2)) return -1;
+	bgzf_mt(fp->x.bam, n_threads, n_sub_blks);
 	return 0;
 }
 
@@ -73,40 +47,76 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 {
 	samfile_t *fp;
 	fp = (samfile_t*)calloc(1, sizeof(samfile_t));
-	if (mode[0] == 'r') {
-		const char *fn_list = (const char*)aux;
+	if (strchr(mode, 'r')) { // read
 		fp->type |= TYPE_READ;
-		if (mode[1] == 'b') { // binary
+		if (strchr(mode, 'b')) { // binary
 			fp->type |= TYPE_BAM;
 			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
+			if (fp->x.bam == 0) goto open_err_ret;
 			fp->header = bam_header_read(fp->x.bam);
-		} else {
+		} else { // text
 			fp->x.tamr = sam_open(fn);
-			fp->header = sam_header_read2(fn_list);
+			if (fp->x.tamr == 0) goto open_err_ret;
+			fp->header = sam_header_read(fp->x.tamr);
+			if (fp->header->n_targets == 0) { // no @SQ fields
+				if (aux) { // check if aux is present
+					bam_header_t *textheader = fp->header;
+					fp->header = sam_header_read2((const char*)aux);
+					if (fp->header == 0) goto open_err_ret;
+					append_header_text(fp->header, textheader->text, textheader->l_text);
+					bam_header_destroy(textheader);
+				}
+				if (fp->header->n_targets == 0 && bam_verbose >= 1)
+					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
+			} else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
 		}
-	} else if (mode[0] == 'w') {
+	} else if (strchr(mode, 'w')) { // write
 		fp->header = bam_header_dup((const bam_header_t*)aux);
-		if (mode[1] == 'b') { // binary
+		if (strchr(mode, 'b')) { // binary
+			char bmode[3];
+			int i, compress_level = -1;
+			for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
+			if (mode[i]) compress_level = mode[i] - '0';
+			if (strchr(mode, 'u')) compress_level = 0;
+			bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
 			fp->type |= TYPE_BAM;
-			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+			fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
+			if (fp->x.bam == 0) goto open_err_ret;
 			bam_header_write(fp->x.bam, fp->header);
-		} else {
-			int i;
-			bam_header_t *alt = 0;
-			alt = bam_header_parse(fp->header->text);
+		} else { // text
+			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
-			if (alt) {
-				if (alt->n_targets != fp->header->n_targets)
-					fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
+			if (fp->x.tamw == 0) goto open_err_ret;
+			if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
+			else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
+			else fp->type |= BAM_OFDEC<<2;
+			// write header
+			if (strchr(mode, 'h')) {
+				int i;
+				bam_header_t *alt;
+				// parse the header text 
+				alt = bam_header_init();
+				alt->l_text = fp->header->l_text; alt->text = fp->header->text;
+				sam_header_parse(alt);
+				alt->l_text = 0; alt->text = 0;
+				// check if there are @SQ lines in the header
+				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
+				if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
+					if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
+						fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
+				} else { // then dump ->target_{name,len}
+					for (i = 0; i < fp->header->n_targets; ++i)
+						fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
+				}
 				bam_header_destroy(alt);
-				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
 			}
-			if (strstr(mode, "h")) // print header
-				for (i = 0; i < fp->header->n_targets; ++i)
-					fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
 		}
 	}
 	return fp;
+
+open_err_ret:
+	free(fp);
+	return 0;
 }
 
 void samclose(samfile_t *fp)
@@ -131,10 +141,46 @@ int samwrite(samfile_t *fp, const bam1_t *b)
 	if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 	if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 	else {
-		char *s = bam_format1(fp->header, b);
+		char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
 		int l = strlen(s);
 		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 		free(s);
 		return l + 1;
 	}
 }
+
+int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+{
+	bam_plbuf_t *buf;
+	int ret;
+	bam1_t *b;
+	b = bam_init1();
+	buf = bam_plbuf_init(func, func_data);
+	bam_plbuf_set_mask(buf, mask);
+	while ((ret = samread(fp, b)) >= 0)
+		bam_plbuf_push(b, buf);
+	bam_plbuf_push(0, buf);
+	bam_plbuf_destroy(buf);
+	bam_destroy1(b);
+	return 0;
+}
+
+char *samfaipath(const char *fn_ref)
+{
+	char *fn_list = 0;
+	if (fn_ref == 0) return 0;
+	fn_list = calloc(strlen(fn_ref) + 5, 1);
+	strcat(strcpy(fn_list, fn_ref), ".fai");
+	if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+		if (access(fn_ref, R_OK) == -1) {
+			fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+		} else {
+			if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n");
+			if (fai_build(fn_ref) == -1) {
+				fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+				free(fn_list); fn_list = 0;
+			}
+		}
+	}
+	return fn_list;
+}