def getSkipUnknownChrString():
    """Necessary for various genotyping steps"""
    return """if [ "$coords" == "unmapped:no_mapped_reads" ]; then
	echo "Input is the unmapped bam... exiting" >> $logFile
	echo no_mapped_reads > $outVcf
	exit 0
else
	echo "Input is not the unmapped bam... continuing" >> $logFile 2>&1
fi

"""
