X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;fp=sam.c;h=b8e7350f3bebd70cd043bf54de02c77315092ee9;hb=9bd8cd7dd42efa091a9361bb06a29d1bead405ce;hp=e8e742c80649f583b16de8fb7b1519eca9a5af10;hpb=d89ec29105e36257fe27067d350ebbe879378c8d;p=samtools.git

diff --git a/sam.c b/sam.c
index e8e742c..b8e7350 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
@@ -152,3 +154,22 @@ 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;
+	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;
+}