From: Heng Li <lh3@live.co.uk>
Date: Wed, 13 May 2009 09:07:55 +0000 (+0000)
Subject:  * samtools-0.1.3-20 (r276)
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=00e380817d6a94c7f6c54d88c56ef8dbfd20b6bb

 * samtools-0.1.3-20 (r276)
 * remove bam1_t::hash again. We need to modify the Perl API anyway to
   make it work with the latest SVN.
 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
---

diff --git a/bam.h b/bam.h
index a784a1f..163dc89 100644
--- a/bam.h
+++ b/bam.h
@@ -190,7 +190,6 @@ typedef struct {
 	bam1_core_t core;
 	int l_aux, data_len, m_data;
 	uint8_t *data;
-	void *hash; // for backward compatibility. It is NEVER used.
 } bam1_t;
 
 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
diff --git a/bam_index.c b/bam_index.c
index 7670c2f..4a41f52 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -268,7 +268,16 @@ bam_index_t *bam_index_load(const char *fn)
 
 	fnidx = (char*)calloc(strlen(fn) + 5, 1);
 	strcpy(fnidx, fn); strcat(fnidx, ".bai");
-	if ((fp = fopen(fnidx, "r")) == 0) {
+	fp = fopen(fnidx, "r");
+	if (fp == 0) { // try "{base}.bai"
+		char *s = strstr(fn, "bam");
+		if (s == fn + strlen(fn) - 3) {
+			strcpy(fnidx, fn);
+			fnidx[strlen(fn)-1] = 'i';
+			fp = fopen(fnidx, "r");
+		}
+	}
+	if (fp == 0) {
 		fprintf(stderr, "[bam_index_load] the alignment is not indexed. Please run `index' command first. Abort!\n");
 		exit(1);
 	}
@@ -327,7 +336,7 @@ bam_index_t *bam_index_load(const char *fn)
 	return idx;
 }
 
-int bam_index_build(const char *fn)
+int bam_index_build2(const char *fn, const char *_fnidx)
 {
 	char *fnidx;
 	FILE *fpidx;
@@ -336,9 +345,16 @@ int bam_index_build(const char *fn)
 	assert(fp = bam_open(fn, "r"));
 	idx = bam_index_core(fp);
 	bam_close(fp);
-	fnidx = (char*)calloc(strlen(fn) + 5, 1);
-	strcpy(fnidx, fn); strcat(fnidx, ".bai");
-	assert(fpidx = fopen(fnidx, "w"));
+	if (_fnidx == 0) {
+		fnidx = (char*)calloc(strlen(fn) + 5, 1);
+		strcpy(fnidx, fn); strcat(fnidx, ".bai");
+	} else fnidx = strdup(_fnidx);
+	fpidx = fopen(fnidx, "w");
+	if (fpidx == 0) {
+		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
+		free(fnidx);
+		return 1;
+	}
 	bam_index_save(idx, fpidx);
 	bam_index_destroy(idx);
 	fclose(fpidx);
@@ -346,13 +362,19 @@ int bam_index_build(const char *fn)
 	return 0;
 }
 
+int bam_index_build(const char *fn)
+{
+	return bam_index_build2(fn, 0);
+}
+
 int bam_index(int argc, char *argv[])
 {
 	if (argc < 2) {
-		fprintf(stderr, "Usage: samtools index <in.bam>\n");
+		fprintf(stderr, "Usage: samtools index <in.bam> [<out.index>]\n");
 		return 1;
 	}
-	bam_index_build(argv[1]);
+	if (argc >= 3) bam_index_build2(argv[1], argv[2]);
+	else bam_index_build(argv[1]);
 	return 0;
 }
 
diff --git a/bamtk.c b/bamtk.c
index 9bb236b..d17cf85 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-19 (r275)"
+#define PACKAGE_VERSION "0.1.3-20 (r276)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);