modified cleanup script; fixed bug in split rmdups

# Juicer version 1.5

total=`ls -l aligned/merged_sort.txt | awk '{print $5}'`

total2=`ls -l aligned/merged_nodups.txt aligned/dups.txt aligned/opt_dups.txt | awk '{sum = sum + $5}END{print sum}'`

if [ $total -eq $total2 ]; then rm aligned/merged_sort.txt; rm -r splits; else echo "Problem: The sum of merged_nodups and the dups files is not the same size as merged_sort.txt"; fi

#bzip2 fastq/*.fastq

if [ $total -eq $total2 ] 

then 

    rm aligned/merged_sort.txt 

    rm -r splits 

    for i in fastq/*.fastq

    do

        gzip $i

    done

    gzip aligned/merged_nodups.txt

    gzip aligned/dups.txt

    gzip aligned/opt_dups.txt

    gzip aligned/abnormal.sam

    gzip aligned/collisions.txt

    gzip aligned/unmapped.sam

else 

    echo "Problem: The sum of merged_nodups and the dups files is not the same size as merged_sort.txt"

    echo "Did NOT clean up";

fi

#!/usr/bin/awk -f

##########

#The MIT License (MIT)

#

# Copyright (c) 2015 Aiden Lab

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

# in the Software without restriction, including without limitation the rights

# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

# copies of the Software, and to permit persons to whom the Software is

# furnished to do so, subject to the following conditions:

#

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

#

#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Dedup script that submits deduping jobs after splitting at known 

# non-duplicate

# Juicer version 1.5

BEGIN{

	tot=0;

	name=0;

		if (p1 != $1 || p2 != $2 || p4 != $4 || p5 != $5 || p8 != $8) {

			sname = sprintf("%s_msplit%04d_", groupname, name);

			sscriptname = sprintf("%s/.%s.slurm", outDir, sname);

			printf("#!/bin/bash -l\n#SBATCH -o %s/dup-split-%s.out\n#SBATCH -e %s/dup-split-%s.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;awk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\ndate\n", outDir, name, outDir, name, queue, groupname, juicedir, dir, sname, dir, name) > sscriptname;

			printf("#!/bin/bash -l\n#SBATCH -o %s/dup-split-%s.out\n#SBATCH -e %s/dup-split-%s.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;awk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\necho Reads:%s\ndate\n", outDir, name, outDir, name, queue, groupname, juicedir, dir, sname, dir, name, tot) > sscriptname;

			sysstring = sprintf("sbatch %s", sscriptname);

			system(sysstring);

			outname = sprintf("%s/split%04d", dir, name);

			close(outname);

			close(sscriptname);

			name++;

			tot=0;

		}

END {

	sname = sprintf("%s_msplit%04d_", groupname, name);

	sscriptname = sprintf("%s/.%s.slurm", outDir, sname);

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-split-%s.out\n#SBATCH -e %s/dup-split-%s.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;awk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\ndate\n", outDir, name, outDir, name, queue, groupname, juicedir, dir, sname, dir, name) > sscriptname;

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-split-%s.out\n#SBATCH -e %s/dup-split-%s.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;awk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\necho Reads:%s\ndate\n", outDir, name, outDir, name, queue, groupname, juicedir, dir, sname, dir, name, tot) > sscriptname;

	sysstring = sprintf("sbatch %s", sscriptname);

	system(sysstring);

	close(sscriptname);

	sscriptname = sprintf("%s/.%s_msplit.slurm", outDir, groupname);

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-merge.out\n#SBATCH -e %s/dup-merge.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -d singleton\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;\necho \"\"; cat %s/%s_msplit*_optdups.txt > %s/opt_dups.txt;cat %s/%s_msplit*_dups.txt > %s/dups.txt;cat %s/%s_msplit*_merged_nodups.txt > %s/merged_nodups.txt;\ndate\n", outDir, outDir, queue, groupname, dir, groupname, dir, dir, groupname, dir, dir, groupname, dir) > sscriptname;

	sysstring = sprintf("sbatch %s", sscriptname);

	system(sysstring);

	close(sscriptname);

	sscriptname = sprintf("%s/.%s_rmsplit.slurm", outDir, groupname);

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-rm.out\n#SBATCH -e %s/dup-rm.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -d singleton\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;\nrm %s/*_msplit*_optdups.txt; rm %s/*_msplit*_dups.txt; rm %s/*_msplit*_merged_nodups.txt;rm %s/split*;\ndate\n", outDir, outDir, queue, groupname, dir, dir, dir, dir) > sscriptname;

	sysstring = sprintf("sbatch %s", sscriptname);

	system(sysstring);

	close(sscriptname);

	sscriptname = sprintf("%s/.%s_finalize.slurm", outDir, groupname);

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-guard-trigger.out\n#SBATCH -e %s/dup-guard-trigger.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -d singleton\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\necho %s %s %s %s;\nsqueue -u %s;\ndate\n", outDir, outDir, queue, groupname, topDir, site, genomeID, genomePath, user, user) > sscriptname;

	var = gensub("[^0-9]", "", "g", maildupid);

	sysstring = sprintf("scontrol update JobID=%s dependency=afterok:%s", guardjid, var);

	system(sysstring);

	close(sscriptname);

	sscriptname = sprintf("%s/.%s_mail.slurm", outDir, groupname);

	printf("#!/bin/bash -l\n#SBATCH -o %s/dup-mail.out\n#SBATCH -e %s/dup-mail.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -d singleton\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;\necho %s %s %s %s | mail -r Juicer@rice.edu -s \"Juicer pipeline finished successfully @ Rice\" -t %s@rice.edu;\ndate\n", outDir, outDir, queue, groupname, topDir, site, genomeID, genomePath, user) > sscriptname;

	sysstring = sprintf("sbatch %s", sscriptname);

	system(sysstring);

	close(sscriptname);

}