test (2f3aaab0) · Commits · Chaos / chaos.juicer

hic_local.sh

+14 −14

Original line number	Diff line number	Diff line
		@@ -151,8 +151,8 @@ do

		rm $rep_dedup_sam

		export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}"
		export _JAVA_OPTIONS="-Xmx60g -Xms60g"
		# export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}"
		# export _JAVA_OPTIONS="-Xmx60g -Xms60g"

		if [ ! -e $rep_stat_m ];then
		dups=$(\
		@@ -182,18 +182,18 @@ do
		$genome_size_file
		fi

		if [ ! -e $rep_hic ];then
		$hic_tools \
		pre \
		--threads $thread_str \
		-s $rep_stat_txt \
		-g $rep_stat_m \
		-i $rep_dedup_index_txt \
		-t $tmp_dir \
		$rep_dedup_txt \
		$rep_hic \
		$genome_size_file
		fi
		# if [ ! -e $rep_hic ];then
		# $hic_tools \
		# pre \
		# --threads $thread_str \
		# -s $rep_stat_txt \
		# -g $rep_stat_m \
		# -i $rep_dedup_index_txt \
		# -t $tmp_dir \
		# $rep_dedup_txt \
		# $rep_hic \
		# $genome_size_file
		# fi
		done