diff --git a/pydeeptools/deeptools/alignmentSieve2.py b/pydeeptools/deeptools/alignmentSieve2.py index 49957f81ca..55fe0b0fbc 100644 --- a/pydeeptools/deeptools/alignmentSieve2.py +++ b/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, diff --git a/pydeeptools/deeptools/bamCompare2.py b/pydeeptools/deeptools/bamCompare2.py index 88281554c2..ff80995821 100644 --- a/pydeeptools/deeptools/bamCompare2.py +++ b/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 diff --git a/pydeeptools/deeptools/bamCoverage2.py b/pydeeptools/deeptools/bamCoverage2.py index 40b2e0248b..b8fd97ffce 100644 --- a/pydeeptools/deeptools/bamCoverage2.py +++ b/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 diff --git a/pydeeptools/deeptools/multiBamSummary2.py b/pydeeptools/deeptools/multiBamSummary2.py index df752f8f1b..25766acdc9 100644 --- a/pydeeptools/deeptools/multiBamSummary2.py +++ b/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,