Loading hic_local.sh +19 −46 Original line number Diff line number Diff line Loading @@ -6,31 +6,26 @@ $pigz_cmd ${work_dir}/*.fastq fastq_suffix=fastq.gz fastq_dir=${work_dir}/fastq split_dir=${work_dir}/splits tmp_dir=${work_dir}/HIC_tmp out_dir=${work_dir}/result if [ ! -d $fastq_dir ];then mkdir -p $fastq_dir;fi if [ ! -d $split_dir ];then mkdir -p $split_dir;fi if [ ! -d $out_dir ];then mkdir -p $out_dir;fi if [ ! -d $tmp_dir ];then mkdir -p $tmp_dir;fi ls ${work_dir}/*_read1.${fastq_suffix} | while read i ls ${work_dir}/*_read1.${fastq_suffix} | while read read1_file do sample=$(basename $i _read1.${fastq_suffix}) j=${work_dir}/${sample}_read2.${fastq_suffix} sample=$(basename $read1_file _read1.${fastq_suffix}) read2_file=${work_dir}/${sample}_read2.${fastq_suffix} if [ ! -e $j ];then echo "$j doesn't exist" if [ ! -e $read2_file ];then echo "$read2_file doesn't exist" stop fi mv $i ${fastq_dir} read1_file=${fastq_dir}/${sample}_read1.${fastq_suffix} read2_file=${fastq_dir}/${sample}_read2.${fastq_suffix} split_prefix=${split_dir}/${sample} out_prefix=${out_dir}/${sample} res_file=${split_prefix}_norm.txt.res.txt Loading Loading @@ -58,23 +53,18 @@ do echo "$num2" > $linecount_file fi if [ ! -e ${split_prefix}.sam ];then if [ ! -e ${split_prefix}.bam ];then $bwa_cmd \ mem \ -SP5M \ -t $thread_str \ $bwa_index \ $read1_file \ $read2_file \ > ${split_prefix}.sam fi if [ ! -e ${split_prefix}.bam ];then $read2_file | \ $awk_cmd \ -v stem=${split_prefix}_norm \ -v site_file=$site_file \ -f ${common_dir}/chimeric_sam.awk \ ${split_prefix}.sam | \ -f ${common_dir}/chimeric_sam.awk | \ $samtools_cmd \ sort \ -t cb \ Loading Loading @@ -110,23 +100,18 @@ do ${split_dir}/${rep}*.bam fi if [ ! -e $rep_dedup_sam ];then if [ ! -e $rep_dedup_txt ];then $samtools_cmd \ view \ -@ $thread_str \ -h $rep_bam | \ $awk_cmd \ -f ${common_dir}/dups_sam.awk \ > $rep_dedup_sam fi if [ ! -e $rep_dedup_txt ];then -f ${common_dir}/dups_sam.awk | \ $samtools_cmd \ view \ -@ $thread_str \ -F 1024 \ -O sam \ $rep_dedup_sam | \ -O sam | \ $awk_cmd \ -v mapq=1 \ -f ${common_dir}/sam_to_pre.awk \ Loading @@ -141,16 +126,14 @@ do fi if [ ! -e $rep_dedup_bam ];then $samtools_cmd view -b -@ $thread_str $rep_dedup_sam $samtools_cmd \ view \ -b \ -@ $thread_str \ $rep_dedup_sam \ > $rep_dedup_bam fi rm $rep_dedup_sam # export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}" # export _JAVA_OPTIONS="-Xmx60g -Xms60g" Loading Loading @@ -232,17 +215,12 @@ do -@ $thread_str \ -h $lib_bam | \ $awk_cmd \ -f ${common_dir}/dups_sam.awk \ > $lib_dedup_sam fi if [ ! -e $lib_dedup_sam ];then -f ${common_dir}/dups_sam.awk | \ $samtools_cmd \ view \ -@ $thread_str \ -F 1024 \ -O sam \ $lib_dedup_sam | \ -O sam | \ $awk_cmd \ -v mapq=1 \ -f ${common_dir}/sam_to_pre.awk \ Loading @@ -265,11 +243,6 @@ do > $lib_dedup_bam fi rm $lib_dedup_sam export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}" export _JAVA_OPTIONS="-Xmx60g -Xms60g" if [ ! -e $lib_stat_m ];then dups=$(\ $samtools_cmd \ Loading Loading
hic_local.sh +19 −46 Original line number Diff line number Diff line Loading @@ -6,31 +6,26 @@ $pigz_cmd ${work_dir}/*.fastq fastq_suffix=fastq.gz fastq_dir=${work_dir}/fastq split_dir=${work_dir}/splits tmp_dir=${work_dir}/HIC_tmp out_dir=${work_dir}/result if [ ! -d $fastq_dir ];then mkdir -p $fastq_dir;fi if [ ! -d $split_dir ];then mkdir -p $split_dir;fi if [ ! -d $out_dir ];then mkdir -p $out_dir;fi if [ ! -d $tmp_dir ];then mkdir -p $tmp_dir;fi ls ${work_dir}/*_read1.${fastq_suffix} | while read i ls ${work_dir}/*_read1.${fastq_suffix} | while read read1_file do sample=$(basename $i _read1.${fastq_suffix}) j=${work_dir}/${sample}_read2.${fastq_suffix} sample=$(basename $read1_file _read1.${fastq_suffix}) read2_file=${work_dir}/${sample}_read2.${fastq_suffix} if [ ! -e $j ];then echo "$j doesn't exist" if [ ! -e $read2_file ];then echo "$read2_file doesn't exist" stop fi mv $i ${fastq_dir} read1_file=${fastq_dir}/${sample}_read1.${fastq_suffix} read2_file=${fastq_dir}/${sample}_read2.${fastq_suffix} split_prefix=${split_dir}/${sample} out_prefix=${out_dir}/${sample} res_file=${split_prefix}_norm.txt.res.txt Loading Loading @@ -58,23 +53,18 @@ do echo "$num2" > $linecount_file fi if [ ! -e ${split_prefix}.sam ];then if [ ! -e ${split_prefix}.bam ];then $bwa_cmd \ mem \ -SP5M \ -t $thread_str \ $bwa_index \ $read1_file \ $read2_file \ > ${split_prefix}.sam fi if [ ! -e ${split_prefix}.bam ];then $read2_file | \ $awk_cmd \ -v stem=${split_prefix}_norm \ -v site_file=$site_file \ -f ${common_dir}/chimeric_sam.awk \ ${split_prefix}.sam | \ -f ${common_dir}/chimeric_sam.awk | \ $samtools_cmd \ sort \ -t cb \ Loading Loading @@ -110,23 +100,18 @@ do ${split_dir}/${rep}*.bam fi if [ ! -e $rep_dedup_sam ];then if [ ! -e $rep_dedup_txt ];then $samtools_cmd \ view \ -@ $thread_str \ -h $rep_bam | \ $awk_cmd \ -f ${common_dir}/dups_sam.awk \ > $rep_dedup_sam fi if [ ! -e $rep_dedup_txt ];then -f ${common_dir}/dups_sam.awk | \ $samtools_cmd \ view \ -@ $thread_str \ -F 1024 \ -O sam \ $rep_dedup_sam | \ -O sam | \ $awk_cmd \ -v mapq=1 \ -f ${common_dir}/sam_to_pre.awk \ Loading @@ -141,16 +126,14 @@ do fi if [ ! -e $rep_dedup_bam ];then $samtools_cmd view -b -@ $thread_str $rep_dedup_sam $samtools_cmd \ view \ -b \ -@ $thread_str \ $rep_dedup_sam \ > $rep_dedup_bam fi rm $rep_dedup_sam # export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}" # export _JAVA_OPTIONS="-Xmx60g -Xms60g" Loading Loading @@ -232,17 +215,12 @@ do -@ $thread_str \ -h $lib_bam | \ $awk_cmd \ -f ${common_dir}/dups_sam.awk \ > $lib_dedup_sam fi if [ ! -e $lib_dedup_sam ];then -f ${common_dir}/dups_sam.awk | \ $samtools_cmd \ view \ -@ $thread_str \ -F 1024 \ -O sam \ $lib_dedup_sam | \ -O sam | \ $awk_cmd \ -v mapq=1 \ -f ${common_dir}/sam_to_pre.awk \ Loading @@ -265,11 +243,6 @@ do > $lib_dedup_bam fi rm $lib_dedup_sam export IBM_JAVA_OPTIONS="-Xmx60g -Xgcthreads${thread_str}" export _JAVA_OPTIONS="-Xmx60g -Xms60g" if [ ! -e $lib_stat_m ];then dups=$(\ $samtools_cmd \ Loading
