Fix #574

CHANGES.txt

@@ -10,6 +10,7 @@
  * Symbol colors for `plotPCA` can now be specified. (issue #560)
  * `plotFingerprint` always returns the synthetic JSD, even if no `--JSDsample` is specified. (issue #564)
  * `plotEnrichment` will only read in annotation files a single time rather than in each thread. This prevents terrible performance when using many tens of millions of BED/GTF regions at the expense of a slight memory increase. (issue #530)
+ * Fixed a small bug generally affecting `plotFingerprint` where BAM files without an index were processed as bigWig files, resulting in a confusing error message (issue #574). Thanks to Sitanshu Gakkhar for poiting this out!
 
 2.5.3
 

deeptools/countReadsPerBin.py

@@ -278,6 +278,8 @@ def run(self, allArgs=None):
         for x in self.bamFilesList:
             try:
                 y = bamHandler.openBam(x)
+            except SystemExit:
+                sys.exit(sys.exc_info()[1])
             except:
                 y = pyBigWig.open(x)
             bamFilesHandlers.append(y)
@@ -424,6 +426,8 @@ def count_reads_in_region(self, chrom, start, end, bed_regions_list=None):
         for fname in self.bamFilesList:
             try:
                 bam_handlers.append(bamHandler.openBam(fname))
+            except SystemExit:
+                sys.exit(sys.exc_info()[1])
             except:
                 bam_handlers.append(pyBigWig.open(fname))