#!/bin/bash

# also add genrichA20Q05.stats_mgm4_atac1.jammanorm_counts.bb

for i in 1; do 
grep -A21 "track[ ]* ATAC$" trackDb_atac.txt && \
grep -A15 "track [ ]* atac_.*" trackDb_atac.txt && \
grep -A11 "track .*1_GenrichAtac_pileup\|track .*12_GenrichAtac_A20_Q0_05" trackDb_atac.txt | \
grep -v "[-][-]" 
done > trackDb_22apr2022.txt

# convert coverage

## from
# atac-SW13-UT1.nsorted.mapped.GenrichAtac.pileup.bw

## to
#  atac-SW13-Dox.GenrichAtac.pileup.merged.bw

perl -pi -e 's/1.nsorted.mapped.GenrichAtac.pileup.bw/.GenrichAtac.pileup.merged.bw/;' trackDb_22apr2022.txt
perl -pi -e 's/SW13-(iBRG1|iHSA)(.+bw)/$1$2/;' trackDb_22apr2022.txt
perl -pi -e 's/.nsorted.mapped.GenrichAtac.A20_Q0.05_P0.05_L0_G100.bb/.GenrichAtac_A20Q05.bb/;' trackDb_22apr2022.txt
perl -pi -e 's/GPP=GenrichPeak_peak/SLICEJAM=slicejam_peak/;s/type=GA[PC]/type=GA/;s/GAC=GenrichAtac_pileup/GA=GenrichAtac/;' trackDb_22apr2022.txt
perl -pi -e 'sub BEGIN {$val="JUNC"};if ($_ =~ / JUNC/) {s/ JUNC/ $val/;if ($val eq "COV"){$val = "PEAK";}else{$val = "COV"}}' trackDb_22apr2022.txt
cat trackDb_slicejam.txt >> trackDb_22apr2022.txt