#samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai test.sam  | samtools sort -o - - > test.bam
#samtools index test.bam
echo "bam done"
/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/readAttributesTC.pl test.sam > test.attr
echo "attr done"
../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.attr > test.readcsv
echo "readcsv done"
../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.clusters | ../scripts/PARclusters2bed.py > test.clusterbed
echo "clusterbed done"
../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.groups | ../scripts/PARclusters2bed.py > test.groupbed
echo "groupbed done"
/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/reads2bed.py test.readcsv > test.readbed
echo "readbed done"
intersectBed -a test.readbed -b test.clusterbed -wao -s | 		awk -F "	" 'BEGIN{OFS=",";} { print  		$5,$7,$8,$9,$11,$12}' | sed '/,\-1/d' | 		/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/editClustersTC.pl .6 > test.clusters.csv
echo "# Stage visbed"
cat test.clusters.csv | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/visclusterbed.py > test.clusters.bed
echo "# Stage geneLvl"
perl /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/geneLevel.pl test.clusters.csv /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/files/gencode.v11.annotation.gtf > test.gene_cl.csv
echo "gene_cl.csv done"
intersectBed -a test.readbed -b test.groupbed -wao -s | 		awk -F "	" 'BEGIN{OFS=",";} { print  		$5,$7,$8,$9,$11,$12}' | sed '/,\-1/d' | 		/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/editClustersTC.pl > test.groups.csv
echo "# Stage geneLvlGroups"
perl /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/geneLevel.pl test.groups.csv /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/files/gencode.v11.annotation.gtf > test.gene_gr.csv
echo "# Stage statsTable"
/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/extractDataTC_MR1.pl test > test.clusters.txt
echo "clusters.txt"
perl /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/Spatial.pl -g /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/files/gencode.v11.annotation.gtf -a test -strict