Merge pull request #1391 from deeptools/ctrl_c

drop the python signal to allow killing rust

Author: WardDeb

pydeeptools/deeptools/alignmentSieve2.py

@@ -3,7 +3,7 @@
 import pysam
 import os
 import sys
-
+import signal
 from deeptools import parserCommon
 from deeptools.bamHandler import openBam
 from deeptools.mapReduce import mapReduce
@@ -343,7 +343,7 @@ def main(args=None):
     # Remove args:
     # label, smartLabels, genomeChunkLength, ignoreDuplicates.
 
-    print(args)
+    signal.signal(signal.SIGINT, signal.SIG_DFL)
     r_alignmentsieve(
         args.bam,
         args.outFile,

pydeeptools/deeptools/bamCompare2.py

@@ -1,6 +1,7 @@
 import argparse
 from deeptools import parserCommon
 from deeptools.hp import r_bamcompare
+import signal
 
 def parseArguments():
     parentParser = parserCommon.getParentArgParse()
@@ -275,7 +276,7 @@ def main(args=None):
         args.blackListFileName = args.blackListFileName[0]
 
     args.pseudocount = 1
-    
+    signal.signal(signal.SIGINT, signal.SIG_DFL)
     r_bamcompare(
         args.bamfile1, # bam file 1
         args.bamfile2, # bam file 2

pydeeptools/deeptools/bamCoverage2.py

@@ -2,6 +2,7 @@
 from deeptools import parserCommon
 from deeptools.hp import r_bamcoverage
 import sys
+import signal
 
 def parseArguments():
     parentParser = parserCommon.getParentArgParse()
@@ -172,7 +173,7 @@ def main(args=None):
     if not args.region:
         args.region = 'None'
     print(args)
-
+    signal.signal(signal.SIGINT, signal.SIG_DFL)
     r_bamcoverage(
         args.bam, # bam file
         args.outFileName, # output file

pydeeptools/deeptools/multiBamSummary2.py

@@ -5,6 +5,7 @@
 import sys
 import argparse
 import numpy as np
+import signal
 
 import deeptools.countReadsPerBin as countR
 from deeptools import parserCommon
@@ -256,7 +257,8 @@ def main(args=None):
 
     """
     args = process_args(args)
-    print(f"args = {args}")
+    
+    signal.signal(signal.SIGINT, signal.SIG_DFL)
     r_mbams(
         args.command,
         args.bamfiles,