#!/usr/bin/perl

$stroot = "CnT01";
$shortLab = "CnT Pol2-ps2 NS20181";
$longLab = "CUTnTag Normalized Depth Tracks - Pol2-pS2 NS20181";

$prio = 100;

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

$datadir = "data/CnT_Pol2-pS2_NS20181";
$trackname = "trackDb.$stroot.txt";

@groups = ("Scri","TP8i");
@reps = (1,2,3);

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

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 CUTnTag=CUTnTag\n";
print OUT "subGroup2\tgrp Group"; foreach $grp (@groups) { print OUT " $grp=$grp"; } print OUT "\n";
print OUT "subGroup3\trep Replicate"; foreach $r (@reps) { print OUT " $r=$r"; } print OUT "\n";
print OUT "dimensions\tdimX=grp dimY=rep\n";
print OUT "sortOrder\tview=+ grp=+ rep=+\n";
print OUT "configurable\ton\n";
print OUT "type\tbigWig\n\n";

# write header for 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\tCUTnTag\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\t0:5\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write depth tracks
foreach $grp (@groups) { foreach $r (@reps) {
  $id = "$grp"."-$r"."-pS2";
  $label_id = "Pol2-pS2.$grp.rep$r";
  $bwfile = "$datadir/$id.hg38.bwt2.MAPQ5-PP.rmdup.singlefragAll.norm5M.bigWig";
  unless (-e $bwfile) { print "WARNING: Did not find \'$bwfile\'.\n"; next; }
  $prio++;
  print OUT "      track\t$label_id\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$label_id\n";
  print OUT "      longLabel\t$grp\-$r\-Pol2-pS2 normalized depth\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tview=CUTnTag grp=$grp rep=$r\n\n";
} }

print OUT "\n\n";

close(OUT);