src/hg/lib/bamFile.c 1.10

Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 4 -r1.9 -r1.10
--- src/hg/lib/bamFile.c	24 Sep 2009 04:33:50 -0000	1.9
+++ src/hg/lib/bamFile.c	8 Oct 2009 06:38:23 -0000	1.10
@@ -44,8 +44,23 @@
 hFreeConn(&conn);
 return fileName;
 }
 
+boolean bamFileExists(char *bamFileName)
+/* Return TRUE if we can successfully open the bam file and its index file. */
+{
+samfile_t *fh = samopen(bamFileName, "rb", NULL);
+if (fh != NULL)
+    {
+    bam_index_t *idx = bam_index_load(bamFileName);
+    samclose(fh);
+    if (idx == NULL)
+	return FALSE;
+    return TRUE;
+    }
+return FALSE;
+}
+
 void bamFetch(char *bamFileName, char *position, bam_fetch_f callbackFunc, void *callbackData)
 /* Open the .bam file, fetch items in the seq:start-end position range,
  * and call callbackFunc on each bam item retrieved from the file plus callbackData. 
  * Note: if sequences in .bam file don't begin with "chr" but cart position does, pass in 
@@ -57,10 +72,10 @@
 
 int chromId, start, end;
 int ret = bam_parse_region(fh->header, position, &chromId, &start, &end);
 if (ret != 0)
-    errAbort("bam_parse_region(%s) failed (%d)", position, ret);
-//?? Could this happen if there is no data on some _random?  can avoid with tdb chromosomes...
+    // If the bam file does not cover the current chromosome, OK
+    return;
 
 bam_index_t *idx = bam_index_load(bamFileName);
 if (idx == NULL)
     errAbort("bam_index_load(%s) failed.", bamFileName);