Description: Fix compatibility with pysam 0.9.0
Author: Afif Elghraoui <afif@debian.org>
Forwarded: no
Last-Update: 2016-03-10
--- python-pbcore.orig/pbcore/io/dataset/utils.py
+++ python-pbcore/pbcore/io/dataset/utils.py
@@ -125,11 +125,11 @@
     shutil.move(tmpname, fname)
 
 def _indexBam(fname):
-    pysam.index(fname)
+    pysam.samtools.index(fname, catch_stdout=False)
     return fname + ".bai"
 
 def _indexFasta(fname):
-    pysam.faidx(fname)
+    pysam.samtools.faidx(fname, catch_stdout=False)
     return fname + ".fai"
 
 def _mergeBams(inFiles, outFile):