#!/usr/bin/perl

$stroot = "ATAC4";
$shortLab = "ATAC-BRM014_dosage";
$longLab = "ATAC Normalized Depth Tracks (BRM014 dosage test)";

$prio = 275;

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

$datadir = "data/ATAC-BRM014_dosage_test";
$trackname = "trackDb.$stroot.txt";

@samples = ("brm014_025uM","brm014_05uM","brm014_1uM","brm014_2uM","brm014_4uM","brm014_8uM","dmso_025ul","dmso_05ul","dmso_1ul","dmso_2ul","dmso_4ul","dmso_8ul");
%nameMod = ("brm014_025uM" => "brm014_0.25uM", "brm014_05uM" => "brm014_0.5uM", "dmso_025ul" => "dmso_0.25ul", "dmso_05ul" => "dmso_0.5ul");

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

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\ttrt Treatment brm014=brm014 dmso=dmso\n";
print OUT "dimensions\tdimX=trt\n";
print OUT "sortOrder\tview=+ trt=+\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 $s (@samples) {
  $id = "atac.wt.treatment_$s.dox";
  if (exists $nameMod{$s}) { $idText = "atac.wt.$nameMod{$s}.dox"; $sText = $nameMod{$s}; } else { $idText = $id; $sText = $s; }
  if ($s =~ /brm/) { $trt = "brm014"; } elsif ($s =~ /dmso/) { $trt = "dmso"; } else { print "error -- treatment\n"; exit; }
  $bwfile = "$datadir/$id.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$idText\n";
  print OUT "      longLabel\twt/dox (treatment:$sText) 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\n\n";
}

print OUT "\n\n";

close(OUT);