X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=ecdee02dddb98a32d47a59e3154179356acecadf;hb=4967051aa734ece6ce44f0fb891a936e849c2fe2;hp=e8e742c80649f583b16de8fb7b1519eca9a5af10;hpb=6f6733c7551a2f4697c46acb4a516fa04bba3e40;p=samtools.git

diff --git a/sam.c b/sam.c
index e8e742c..ecdee02 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)
@@ -54,6 +55,7 @@ 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);
 				}
@@ -61,7 +63,6 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 					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);
 		}
-		sam_header_parse_rg(fp->header);
 	} else if (mode[0] == 'w') { // write
 		fp->header = bam_header_dup((const bam_header_t*)aux);
 		if (mode[1] == 'b') { // binary
@@ -152,3 +153,23 @@ 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 {
+			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;
+}