* 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 a784a1f3f7f919d38e771a38a1a2d7b5d35cde2e..163dc893e192d6eaa9ebfcc3b3b8614d142ca211 100644 (file)
--- 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 7670c2f3f1058af65086cd40f62f3acbd288025d..4a41f5264a67148c75f1f9be6d7e6880e5b848a6 100644 (file)
--- 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 9bb236bf7de20749fc128db8e19152a4925cb7e9..d17cf855d3ee452c07a242d3206f4800817bc0c2 100644 (file)
--- 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[]);