#!/bin/bash
#
#SBATCH --output=/home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/logs/%J.out
#SBATCH --mem=8G
#SBATCH --cpus-per-task=1
#SBATCH --partition=queue0

set -e -o pipefail
TMPDIR=/tmp/$SLURM_JOB_ID
mkdir -p ${TMPDIR}

cut -f1,3 /net/seq/data/genomes/human/GRCh38/noalts/GRCh38_no_alts.chrom.sizes  > ${TMPDIR}/chrom.sizes


# zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.bedgraph.gz | cut -f1-3,4 | awk '$4 > 0 { print; }' > ${TMPDIR}/interval.all.exp.bedgraph
# bedGraphToBigWig ${TMPDIR}/interval.all.exp.bedgraph  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.exp.bw

# zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.bedgraph.gz | cut -f1-3,5 | awk '$4 > 0 { print; }' > ${TMPDIR}/interval.all.obs.bedgraph
# bedGraphToBigWig ${TMPDIR}/interval.all.obs.bedgraph  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.obs.bw

# zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.bedgraph.gz | cut -f1-3,6 > ${TMPDIR}/interval.all.lnpval.bedgraph
# bedGraphToBigWig ${TMPDIR}/interval.all.lnpval.bedgraph  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.lnpval.bw

# zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.bedgraph.gz | cut -f1-3,7 > ${TMPDIR}/interval.all.winlnpval.bedgraph
# bedGraphToBigWig ${TMPDIR}/interval.all.winlnpval.bedgraph  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.winlnpval.bw

# zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.bedgraph.gz | cut -f1-3,8 > ${TMPDIR}/interval.all.fpr.bedgraph
# bedGraphToBigWig ${TMPDIR}/interval.all.fpr.bedgraph ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fpr.bw

zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.05.bed.gz | cut -f1-3 > ${TMPDIR}/interval.all.fps.0.05.bed
bedToBigBed -type=bed3 -tab ${TMPDIR}/interval.all.fps.0.05.bed  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.05.bb

zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.01.bed.gz | cut -f1-3 > ${TMPDIR}/interval.all.fps.0.01.bed
bedToBigBed -type=bed3 -tab ${TMPDIR}/interval.all.fps.0.01.bed  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.01.bb

zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.001.bed.gz | cut -f1-3 > ${TMPDIR}/interval.all.fps.0.001.bed
bedToBigBed -type=bed3 -tab ${TMPDIR}/interval.all.fps.0.001.bed  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.001.bb

zcat /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.0001.bed.gz | cut -f1-3 > ${TMPDIR}/interval.all.fps.0.0001.bed
bedToBigBed -type=bed3 -tab ${TMPDIR}/interval.all.fps.0.0001.bed  ${TMPDIR}/chrom.sizes /home/jvierstra/proj/footprinting.2019/processed/fSkin_Fibroblast-DS19745/interval.all.fps.0.0001.bb

rm -rf ${TMPDIR}