Update scapp.py

Shamir-Lab · Jan 23, 2020 · 5c7e780 · 5c7e780
1 parent 8e85951
commit 5c7e780
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scapp/scapp.py b/scapp/scapp.py
@@ -243,7 +243,7 @@ def main():
         bwa_outfile.flush()
 
         # Sort filtered reads with samtools
-        sorted_reads = os.path.join(int_dir, "reads_pe_primary.sort")
+        sorted_reads = os.path.join(int_dir, "reads_pe_primary.sort.bam")
         cmd = samtools_file + " sort " + primary_bam + ' -o ' + sorted_reads
         logger.info("Executing command: '{}'".format(cmd))
         subprocess.check_call(cmd,stderr=subprocess.STDOUT, stdout=bwa_outfile, shell=True)