CPU additions for justexact option, no fragment maps by default, changes to... (284cb332) · Commits · Chaos / chaos.juicer

CPU/common/countligations.sh

+3 −3

Changes for CPU/common/countligations.sh: 3 added lines, 3 removed lines.
Original line number	Diff line number	Diff line
		@@ -27,10 +27,10 @@
		# Juicer version 1.5
		if [ "$usegzip" -eq 1 ]
		then
		num1=$(paste <(zcat $name1$ext) <(zcat $name2$ext) \| grep -c $ligation)
		num2=$(zcat ${name1}${ext} \| wc -l \| awk '{print $1}')
		num1=$(paste <(gunzip -c $name1$ext) <(gunzip -c $name2$ext) \| grep -cE $ligation)
		num2=$(gunzip -c ${name1}${ext} \| wc -l \| awk '{print $1}')
		else
		num1=$(paste $name1$ext $name2$ext \| grep -c $ligation)
		num1=$(paste $name1$ext $name2$ext \| grep -cE $ligation)
		num2=$(wc -l ${name1}${ext} \| awk '{print $1}')
		fi
		echo -ne "$num1 " > ${name}${ext}_norm.txt.res.txt

CPU/common/dups.awk

+6 −0

Changes for CPU/common/dups.awk: 6 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -50,8 +50,14 @@ function optcheck(tile1,tile2,x1,x2,y1,y2) {
		# Executed once, before beginning the file read
		BEGIN {
		i=0;
		if (length(nowobble) == 0) {
		wobble1=4;
		wobble2=4;
		}
		else {
		wobble1=0;
		wobble2=0;
		}
		# names of output files
		# the variable "name" can be set via the -v flag
		dupname=name"dups.txt";

CPU/juicer.sh

+17 −6

Changes for CPU/juicer.sh: 17 added lines, 6 removed lines.
Original line number	Diff line number	Diff line
		@@ -61,7 +61,7 @@
		shopt -s extglob
		export LC_ALL=C

		juicer_version="1.5.6"
		juicer_version="1.5.7"
		### LOAD BWA AND SAMTOOLS


		@@ -86,10 +86,13 @@ genomeID="hg19"
		shortreadend=0
		# description, default empty
		about=""
		nofrag=0
		# do not include fragment delimited maps by default
		nofrag=1
		# use wobble for dedupping by default (not just exact matches)
		justexact=0

		## Read arguments
		usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-s site] [-a about] [-R end]\n [-S stage] [-p chrom.sizes path] [-y restriction site file]\n [-z reference genome file] [-D Juicer scripts directory]\n [-b ligation] [-t threads] [-r] [-h] [-x]"
		usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-s site] [-a about] [-R end]\n [-S stage] [-p chrom.sizes path] [-y restriction site file]\n [-z reference genome file] [-D Juicer scripts directory]\n [-b ligation] [-t threads] [-r] [-h] [-f] [-j]"
		genomeHelp="* [genomeID] must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \n \"$genomeID\"); alternatively, it can be defined using the -z command"
		dirHelp="* [topDir] is the top level directory (default\n \"$topDir\")\n [topDir]/fastq must contain the fastq files\n [topDir]/splits will be created to contain the temporary split files\n [topDir]/aligned will be created for the final alignment"
		siteHelp="* [site] must be defined in the script, e.g. \"HindIII\" or \"MboI\" \n (default \"$site\")"
		@@ -103,7 +106,8 @@ scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n which
		refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n files must be in same directory"
		ligationHelp="* [ligation junction]: use this string when counting ligation junctions"
		threadsHelp="* [threads]: number of threads when running BWA alignment"
		excludeHelp="* -x: exclude fragment-delimited maps from hic file creation"
		excludeHelp="* -f: include fragment-delimited maps in hic file creation"
		justHelp="* -j: just exact duplicates excluded at dedupping step"
		helpHelp="* -h: print this help and exit"

		printHelpAndExit() {
		@@ -126,7 +130,7 @@ printHelpAndExit() {
		exit "$1"
		}

		while getopts "d:g:R:a:hrs:p:y:z:S:D:xt:b:" opt; do
		while getopts "d:g:R:a:hrs:p:y:z:S:D:fjt:b:" opt; do
		case $opt in
		g) genomeID=$OPTARG ;;
		h) printHelpAndExit 0;;
		@@ -140,9 +144,10 @@ while getopts "d:g:R:a:hrs:p:y:z:S:D:xt:b:" opt; do
		z) refSeq=$OPTARG ;;
		S) stage=$OPTARG ;;
		D) juiceDir=$OPTARG ;;
		x) nofrag=1 ;; #no fragment maps
		f) nofrag=0 ;; #use fragment maps
		b) ligation=$OPTARG ;;
		t) threads=$OPTARG ;;
		j) justexact=1 ;;
		[?]) printHelpAndExit 1;;
		esac
		done
		@@ -503,7 +508,13 @@ then
		touch ${outputdir}/dups.txt
		touch ${outputdir}/optdups.txt
		touch ${outputdir}/merged_nodups.txt

		if [ "$justexact" -eq 1 ]
		then
		awk -f ${juiceDir}/scripts/common/dups.awk -v name=${outputdir}/ -v nowobble=1 ${outputdir}/merged_sort.txt
		else
		awk -f ${juiceDir}/scripts/common/dups.awk -v name=${outputdir}/ ${outputdir}/merged_sort.txt
		fi
		# for consistency with cluster naming in split_rmdups
		mv ${outputdir}/optdups.txt ${outputdir}/opt_dups.txt
		fi

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