#!/usr/bin/perl

$stroot = "AgCC.ATAC.P";
$shortLab = "AgingCC ATAC Peaks";
$longLab = "AgingCC ATAC Peaks";

$prio = 250;

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

$datadir = "data/ATAC_peaks";
$trackname = "trackDb.$stroot.txt";

@comparisons = ("APC_Tumor_byAge","APC_Crypt_byAge","APC_SI_byAge","APC_Sorted_byAge","AKPS_Tumor_byAge","YoungTumorVsYoungCrypt","OldTumorVsOldCrypt");


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

open(OUT, ">$trackname");

##### unified peak #####
# 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 APK=ATACpeaks\n";
print OUT "subGroup2\ttype Type uni=unified diffPk=diffPk\n";
#print OUT "sortOrder\tType=+\n";
print OUT "type\tbigBed\n\n";

# write header for peak tracks
print OUT "   track\tdata$stroot\_Peaks\n";
print OUT "   parent\tdata$stroot\n";
print OUT "   shortLabel\t$shortLab\n";
print OUT "   longLabel\t$longLab\n";
print OUT "   view\tAPK\n";
print OUT "   visibility\tdense\n";
print OUT "   type\tbigBed 3\n";
print OUT "   allButtonPair\ton\n";
print OUT "   centerLabelsDense\ton\n";
print OUT "   dragAndDrop\ton\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";


# write unified peak tracks...
  $bbfile = "$datadir/unified-ATAC.N10.canonAutoXY.min50bp.ExclBlacklist.bigBed";
  unless (-e $bbfile) { print "ERROR: Did not find $bbfile.\n"; exit; }
  $prio++;
  print OUT "      track\tuniATAC.$stroot\n";
  print OUT "      parent\tdata$stroot\_Peaks\n";
  print OUT "      bigDataUrl\t$bbfile\n";
  print OUT "      shortLabel\tATAC unified peaks\n";
  print OUT "      longLabel\tATAC unified peaks (10+ overlap)\n";
  print OUT "      type\tbigBed 3\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\tdense\n";
  print OUT "      subGroups\tView=APK type=uni\n\n";


# write differential peak tracks...
  $C = 0;
  foreach $cmp (@comparisons) { $C++;
    $bbfile = "$datadir/diffPeaks-EdgeR.fdr1e-3.minRPKM.ATAC.$cmp.bigBed";
    unless (-e $bbfile) { print "ERROR: Did not find $bbfile.\n"; exit; }
    $prio++;
    print OUT "      track\tdiff$C.ATAC.$stroot\n";
    print OUT "      parent\tdata$stroot\_Peaks\n";
    print OUT "      bigDataUrl\t$bbfile\n";
    print OUT "      shortLabel\tATAC $cmp diffPk\n";
    print OUT "      longLabel\tATAC $cmp differential peaks (EdgeR 1e-3, minRPKM)\n";
    print OUT "      type\tbigBed 9\n";
    print OUT "      itemRgb on\n";
    print OUT "      priority\t$prio\n";
    print OUT "      visibility\tdense\n";
    print OUT "      subGroups\tView=APK type=diffPk\n\n";
  }


close(OUT);