X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=sam.c;h=f026bc80864dbc75557bf632c760978e54acc453;hp=45cb05cf3dd6f8a04acfd4dd92c8d250835855a2;hb=e2bd290b8643f0a728c282a8b825392307750210;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/sam.c b/sam.c
index 45cb05c..f026bc8 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);
@@ -19,7 +21,6 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 		h->target_len[i] = h0->target_len[i];
 		h->target_name[i] = strdup(h0->target_name[i]);
 	}
-	if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
 	return h;
 }
 static void append_header_text(bam_header_t *header, char* text, int len)
@@ -39,9 +40,9 @@ 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') { // read
+	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;
@@ -54,19 +55,23 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 				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)
+				if (fp->header->n_targets == 0 && bam_verbose >= 1)
 					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
-			} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
+			} else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
 		}
-		sam_header_parse_rg(fp->header);
-	} else if (mode[0] == 'w') { // write
+	} 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];
-			bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
+			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, bmode) : bam_dopen(fileno(stdout), bmode);
 			if (fp->x.bam == 0) goto open_err_ret;
@@ -75,8 +80,11 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 			if (fp->x.tamr == 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 (strstr(mode, "h")) {
+			if (strchr(mode, 'h')) {
 				int i;
 				bam_header_t *alt;
 				// parse the header text 
@@ -85,10 +93,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 				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);
+				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)
-						fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
+					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]);
@@ -126,7 +134,7 @@ 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);
@@ -149,3 +157,23 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 	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;
+}