simplifying logic for qc and in-situ (514a9baf) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+15 −32

Changes for SLURM/scripts/juicer.sh: 15 added lines, 32 removed lines.
Original line number	Diff line number	Diff line
		@@ -1454,6 +1454,19 @@ FINCLN1`
		exit 0
		fi

		if [ "$qc" = 1 ] \|\| [ "$insitu" = 1 ]
		then
		resstr="-r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000"
		else
		resstr="-r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100"
		fi
		if [ "$nofrag" -eq 1 ]
		then
		fragstr=""
		else
		fragstr="-f $site_file"
		fi

		jid=`sbatch <<- HIC \| egrep -o -e "\b[0-9]+$"
		#!/bin/bash -l
		#SBATCH -p $long_queue
		@@ -1484,22 +1497,7 @@ FINCLN1`
		time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged1.txt 500000 > ${outputdir}/merged1_index.txt
		fi

		if [ "$qc" = 1 ] \|\| [ "$insitu" = 1 ]
		then
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		fi
		else
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		fi
		fi
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $resstr $fragstr $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		time ${juiceDir}/scripts/juicer_tools addNorm $threadNormString ${outputdir}/inter.hic
		rm -Rf ${outputdir}"/HIC_tmp"
		date
		@@ -1536,22 +1534,7 @@ HIC`
		time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged30.txt 500000 > ${outputdir}/merged30_index.txt
		fi

		if [ "$qc" = 1 ] \|\| [ "$insitu" = 1 ]
		then
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		fi
		else
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		fi
		fi
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $resstr $fragstr $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		time ${juiceDir}/scripts/juicer_tools addNorm $threadNormString ${outputdir}/inter_30.hic
		rm -Rf ${outputdir}"/HIC30_tmp"
		date

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