adjustments to paths; do correct things for mnd for single seq (6bbcdd26) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer_arrowhead.sh

+2 −1

Changes for SLURM/scripts/juicer_arrowhead.sh: 2 added lines, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -51,7 +51,7 @@ then
		juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"
		fi

		while getopts "h:j:i:" opt; do
		@@ -77,6 +77,7 @@ fi

		echo -e "${juicer_tools_path} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\n"
		echo -e "ARROWHEAD:\n"
		echo "${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}_contact_domains"
		${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains"
		if [ $? -ne 0 ]; then
		echo "***! Problem while running Arrowhead";

+3 −2

Changes for SLURM/scripts/juicer_hiccups.sh: 3 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -53,8 +53,8 @@ then
		bed_file_dir="/storage/aiden/juicer/references/motif"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer/references/motif"
		juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer2/references/motif"
		fi

		while getopts "h:g:j:i:m:" opt; do
		@@ -83,6 +83,7 @@ fi
		echo -e "\nHiCCUPS:\n"
		if hash nvcc 2>/dev/null
		then
		echo "${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}_loops"
		${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops"
		if [ $? -ne 0 ]; then
		echo "***! Problem while running HiCCUPS";

+2 −2

Changes for SLURM/scripts/juicer_postprocessing.sh: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -55,8 +55,8 @@ then
		bed_file_dir="/storage/aiden/juicer/references/motif"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer/references/motif"
		juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer2/references/motif"
		fi

		while getopts "h:g:j:i:m:" opt; do

+19 −3

Changes for SLURM/scripts/sam_to_pre.awk: 19 added lines, 3 removed lines.
Original line number	Diff line number	Diff line
		@@ -27,6 +27,15 @@ processme != 0 {
		saved_mq = $5;
		saved_cigar = $6;
		saved_chr = $3;
		if (length(singleend)>0) {
		for (ind=12; ind<=NF; ind++) {
		if ($(ind) ~ /^ep:/) {
		split($(ind), ep_str, ":");
		}
		}
		saved_ext = int(ep_str[3]);
		}
		else saved_ext = "";
		next;
		}
		else {
		@@ -54,10 +63,11 @@ processme != 0 {
		else if ($i ~ /^mp/) {
		split($i, mp, ":");
		}
		else if ($i ~ /^rt:/) {
		split($i, rt, ":");
		}
		for (ind=12; ind<=NF; ind++) {
		if ($(ind) ~ /^rt:/) {
		split($(ind), rt, ":");
		else if ($i ~ /^ep:/) {
		split($i, ep_str, ":");
		}
		}
		if (rt[3]%2==0) {
		@@ -87,8 +97,14 @@ processme != 0 {

		# merged_nodups
		if (use_external_pos) {
		if (length(singleend)>0) {
		pos1 = saved_ext;
		pos2 = int(ep_str[3]);
		}
		else {
		pos1 = extpos1;
		pos2 = extpos2;
		}
		print str1, chr1, pos1, frag1, str2, chr2, pos2, frag2, mq1, cigar1, seq1, mq2, cigar2, seq2, $1, $1;
		}
		else {