bug fixes

Author: jodyphelan

pathogenprofiler/bam.py

@@ -77,7 +77,7 @@ def flagstat(self):
         tmpfile = str(uuid4())
         run_cmd(f"samtools flagstat -O json {self.bam_file} > {tmpfile}")
         flagstat = json.load(open(tmpfile))
-        self.num_reads_mapped = flagstat["QC-passed reads"]["primary mapped"]
+        self.num_reads_mapped = flagstat["QC-passed reads"]["mapped"]
         self.pct_reads_mapped = flagstat["QC-passed reads"]["mapped %"]
         return self.num_reads_mapped,self.pct_reads_mapped
 

scripts/add_dummy_AD.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#! /usr/bin/env python3
 import sys
 
 for l in sys.stdin:

scripts/combine_vcf_variants.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#! /usr/bin/env python3
 from collections import defaultdict
 import sys
 import argparse

scripts/rename_vcf_chrom.py

@@ -1,3 +1,4 @@
+#! /usr/bin/env python3
 import pathogenprofiler as pp
 import sys
 import argparse