#!/usr/bin/perl

$stroot = "ATAC3";
$shortLab = "ATAC-BRM014";
$longLab = "ATAC Normalized Depth Tracks (BRM014 final datasets)";

$prio = 270;

##############################################################

$datadir = "data/ATAC-BRM014_final";
$trackname = "trackDb.$stroot.txt";

@inds = ("dox","ctrl");
@trts = ("brm014","dmso");

##############################################################

open(OUT, ">$trackname");

##### normalized depth #####
# write header supertrack header
print OUT "track\tdata$stroot\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\t$shortLab\n";
print OUT "longLabel\t$longLab\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View ATAC=ATAC\n";
print OUT "subGroup2\tind IfInduced"; foreach $ind (@inds) { print OUT " $ind=$ind"; } print OUT "\n";
print OUT "subGroup3\ttrt Treatment"; foreach $trt (@trts) { print OUT " $trt=$trt"; } print OUT "\n";
print OUT "dimensions\tdimX=trt dimY=ind\n";
print OUT "sortOrder\tview=+ trt=+ ind=+\n";
print OUT "configurable\ton\n";
print OUT "type\tbigWig\n\n";

# write header for ATAC tracks
print OUT "   track\tdata$stroot\_ViewDepth\n";
print OUT "   parent\tdata$stroot\n";
print OUT "   shortLabel\t$shortLab\n";
print OUT "   longLabel\t$longLab\n";
print OUT "   view\tATAC\n";
print OUT "   visibility\tfull\n";
print OUT "   type\tbigWig\n";
print OUT "   allButtonPair\ton\n";
print OUT "   centerLabelsDense\ton\n";
print OUT "   dragAndDrop\ton\n";
print OUT "   alwaysZero\ton\n";
print OUT "   graphTypeDefault\tbar\n";
print OUT "   maxHeightPixels\t150:40:11\n";
print OUT "   autoScale\tgroup\n";
#print OUT "   viewLimits\t0:100\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write ATAC depth tracks
foreach $trt (@trts) { foreach $ind (@inds) {
  $id = "atac.wt.treatment_$trt.$ind";
  $bwfile = "$datadir/$id.merged_replicates_coverage.bigWig";
  unless (-e $bwfile) { print "WARNING: Did not find \'$bwfile\'.\n"; next; }
  $prio++;
  print OUT "      track\t$id\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\twt/$ind (treatment:$trt) normalized depth (ATAC)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tview=ATAC trt=$trt ind=$ind\n\n";
} }

print OUT "\n\n";

close(OUT);