remove tmpfile

jodyphelan · Nov 7, 2021 · 73f2461 · 73f2461
1 parent 9e33a61
commit 73f2461
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/pathogenprofiler/bam.py b/pathogenprofiler/bam.py
@@ -3,6 +3,7 @@
 from collections import defaultdict
 import json
 from uuid import uuid4
+import os
 
 class bam:
     """
@@ -79,6 +80,7 @@ def flagstat(self):
         flagstat = json.load(open(tmpfile))
         self.num_reads_mapped = flagstat["QC-passed reads"]["mapped"]
         self.pct_reads_mapped = flagstat["QC-passed reads"]["mapped %"]
+        os.remove(tmpfile)
         return self.num_reads_mapped,self.pct_reads_mapped
 
     def get_median_coverage(self):