Use memory map to speed up genome reference retrival (small fix)

zwdzwd · Mar 21, 2016 · 844e663 · 844e663
1 parent 703d3eb
commit 844e663
Showing 1 changed file with 1 addition and 5 deletions.
diff --git a/transvar/faidx.py b/transvar/faidx.py
@@ -1,7 +1,6 @@
 """ faidx python code adapted from Allen Yu 
 http://www.allenyu.info/item/24-quickly-fetch-sequence-from-samtools-faidx-indexed-fasta-sequences.html """
 import sys
-
 import mmap
 
 from err import *
@@ -88,10 +87,7 @@ def fetch_sequence(self, chrom, start, end):
 
     def __exit__(self, type, value, traceback):
         self.fasta_handle.close()
-
-        if self.use_mmap:
-            self.fasta_fd.close()
-
+        self.fasta_fd.close()
         self.faidx_handle.close()
 
     def chrm2len(self, chrm):