ac6fd0ed90d96f059fabcd906969363e68aaba2e
aamp
  Mon Jul 11 07:33:38 2011 -0700
compile-error fixed: unused var
diff --git src/lib/bamUdc.c src/lib/bamUdc.c
index 3eead98..60dfc86 100644
--- src/lib/bamUdc.c
+++ src/lib/bamUdc.c
@@ -118,31 +118,32 @@
     {
     mkdirTrashDirectory(dirName);
     size_t len = strlen(trashDir()) + 1 + strlen(dirName) + 1;
     samDir = needMem(len);
     safef(samDir, len, "%s/%s", trashDir(), dirName);
     }
 return samDir;
 }
 #endif//ndef KNETFILE_HOOKS
 
 boolean bamFileExistsUdc(char *fileOrUrl, char *udcFuseRoot)
 /* Return TRUE if we can successfully open the bam file and its index file. */
 {
 char *bamFileName = samtoolsFileNameUdcFuse(fileOrUrl, udcFuseRoot);
 samfile_t *fh = samopen(bamFileName, "rb", NULL);
-boolean usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
+boolean usingUrl = TRUE; 
+usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
 if (fh != NULL)
     {
 #ifndef KNETFILE_HOOKS
     // When file is an URL, this caches the index file in addition to validating:
     // Since samtools's url-handling code saves the .bai file to the current directory,
     // chdir to a trash directory before calling bam_index_load, then chdir back.
     char *runDir = getCurrentDir();
     char *samDir = getSamDir();
     if (usingUrl)
 	setCurrentDir(samDir);
 #endif//ndef KNETFILE_HOOKS
     bam_index_t *idx = bam_index_load(bamFileName);
 #ifndef KNETFILE_HOOKS
     if (usingUrl)
 	setCurrentDir(runDir);
@@ -193,31 +194,32 @@
     samclose(*pSamFile);
     *pSamFile = NULL;
     }
 }
 
 void bamFetchUdc(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
 		     samfile_t **pSamFile, char *udcFuseRoot)
 /* 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.
  * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  */
 {
 char *bamFileName = NULL;
 samfile_t *fh = bamOpenUdc(fileOrUrl, &bamFileName, udcFuseRoot);
-boolean usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
+boolean usingUrl = TRUE;
+usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
 if (pSamFile != NULL)
     *pSamFile = fh;
 int chromId, start, end;
 int ret = bam_parse_region(fh->header, position, &chromId, &start, &end);
 if (ret != 0 && startsWith("chr", position))
     ret = bam_parse_region(fh->header, position+strlen("chr"), &chromId, &start, &end);
 if (ret != 0)
     // If the bam file does not cover the current chromosome, OK
     return;
 #ifndef KNETFILE_HOOKS
 // Since samtools' url-handling code saves the .bai file to the current directory,
 // chdir to a trash directory before calling bam_index_load, then chdir back.
 char *runDir = getCurrentDir();
 char *samDir = getSamDir();
 if (usingUrl)