updated shortread test to be consistent across scripts, deleted old jars (79e2c8e7) · Commits · Chaos / chaos.juicer

Original line number	Diff line number	Diff line
		@@ -427,7 +427,7 @@ SPLITEND
		fi
		qsub -o ${topDir}/uger.out -j y -q ${queue} -r y -N ${groupname}${jname}countligations -v ARG1=${usegzip},name=${name},name1=${name1},name2=${name2},ext=${ext},ligation=${ligation} ${juiceDir}/scripts/countligations.sh
		# align read1 fastq
		if [ $shortread ] \|\| [ $shortreadend -eq 1 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 1 ]
		then
		alloc_mem=16
		else
		@@ -440,7 +440,7 @@ SPLITEND
		source $usePath
		$load_bwa
		# Align read1
		if [ $shortread ] \|\| [ $shortreadend -eq 1 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 1 ]
		then
		echo 'Running command bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam'
		bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam
		@@ -468,7 +468,7 @@ SPLITEND
		ALGNR1
		touchfile2=${tmpdir}/${jname}2
		# align read2 fastq
		if [ $shortread ] \|\| [ $shortreadend -eq 2 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 2 ]
		then
		alloc_mem=16
		else
		@@ -480,7 +480,7 @@ ALGNR1
		source $usePath
		$load_bwa
		# Align read2
		if [ $shortread ] \|\| [ $shortreadend -eq 2 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 2 ]
		then
		echo 'Running command bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam '
		bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam

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