#!/usr/bin/perl

### CpG %meth by genotype (supertrack1) [default: B6 & C3 full]
### nonCpG %meth by genotype (supertrack2) [default: off]
### depth by genotype (supertrack3) [default: B6 & C3 full]
### CpG %meth by animal (supertrack4) [default: off]
### nonCpG %meth by animal (supertrack5) [default: off]
### depth by animal (supertrack6) [default: off]
### DMRs (supertrack7) [default: dense]
### genome-specific references (supertrack8) [default: dense]
### FOXA1 ChIPseq (supertrack9) [default: off]

@gts = ("B6_M", "B6_F", "C3_M", "C3_F", "B6C3F1_M", "B6C3F1_F", "C3B6F1_M", "C3B6F1_F");
@reps = (1,2,3);

%gtLabels = (); @animals = (); %aniLabels = ();
foreach $gt (@gts) {
  ($genome, $gender) = split/\_/, $gt;
  $L = "$genome ";
  if ($gender eq "F") { $L .= "female"; }
  elsif ($gender eq "M") { $L .= "male"; }
  else { print "exit error 1.\n"; exit; }
  $gtLabels{$gt} = $L;
  $gtLabels{$gt} .= "s"; #use plural label for genotypes, singular for individual animals
  foreach $rep (@reps) {
    $ani = "$gt"."_$rep";
    push @animals, $ani;
    $LL = "$L animal $rep";
    $aniLabels{$ani} = $LL;
  }
}    


open(OUT, ">trackDb_mousemeth_hub.txt");


#CpG pctMeth by genotype
$supertrack1_name = "st1_mpctCpG_GT";
print OUT "track $supertrack1_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS CpG %Methylation by Genotype\n";
print OUT "longLabel\tPercent methylation at cytosines in CpG context for each genotype, per strand; validated and unvalidated sites are overlayed.  Data from WGBS.\n\n";
$pri=1.0;
foreach	$gt (@gts) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st1_$gt"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack1_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$gt CpG %methylation\n";
  print OUT "\tlongLabel\t$gt CpG %methylation\n";
  print OUT "\ttype bigWig -100 100\n";
  print OUT "\tviewLimits -100:100\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  if ($gt =~ /F1/) { print OUT "\tvisibility hide\n"; } else { print OUT "\tvisibility full\n"; }
  print OUT "\taggregate solidOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:40:11\n";
  print OUT "\tpriority $prio\n\n";

  print OUT "\t\ttrack $mwtrack\VCpG\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CpG.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CpG %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CpG sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility full\n";
  print OUT "\t\tcolor 0,0,204\n\n";#blue
  print OUT "\t\ttrack $mwtrack\UCpG\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CpG.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CpG %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CpG sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility full\n";
  print OUT "\t\tcolor 204,0,0\n\n";#red
}
print OUT "\n\n\n";


#nonCpG pctMeth by genotype
$supertrack2_name = "st2_mpctCHX_GT";
print OUT "track $supertrack2_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS Non-CpG %Methylation by Genotype\n";
print OUT "longLabel\tPercent methylation at cytosines in non-CpG context for each genotype, per context, per strand; validated and unvalidated sites are overlayed.  Data from WGBS.\n\n";
$pri=2.0;
foreach $gt (@gts) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st2_$gt"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack2_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$gt non-CpG %methylation\n";
  print OUT "\tlongLabel\t$gt non-CpG %methylation\n";
  print OUT "\ttype bigWig -100 100\n";
  print OUT "\tviewLimits -100:100\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  print OUT "\tvisbility hide\n";
  print OUT "\taggregate solidOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:40:11\n";
  print OUT "\tpriority $prio\n\n";

  print OUT "\t\ttrack $mwtrack\VCHG\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CHG.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CHG %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CHG sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 153,51,204\n\n";#purple
  print OUT "\t\ttrack $mwtrack\UCHG\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CHG.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CHG %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CHG sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 255,102,0\n\n";#orange

  print OUT "\t\ttrack $mwtrack\VCHH\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CHH.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CHH %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CHH sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 0,102,0\n\n";#darkgreen
  print OUT "\t\ttrack $mwtrack\UCHH\n";
  print OUT "\t\tbigDataUrl DATA/$gt.CHH.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$gt CHH %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CHH sites for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 255,215,0\n\n";#darkyellow

}
print OUT "\n\n\n";



#depth by genotype
$supertrack3_name = "st3_DepthGT";
print OUT "track $supertrack3_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS Depth by Genotype\n";
print OUT "longLabel\tWGBS depth for each genotype, per strand\n\n";
$pri = 3.0;
foreach $gt (@gts) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st3_$gt"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack3_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$gt WGBS depth\n";
  print OUT "\tlongLabel\t$gt WGBS depth\n";
  print OUT "\ttype bigWig\n";
  print OUT "\tviewLimits 0:100\n";
  print OUT "\twindowingFunction mean\n";
  print OUT "\tgridDefault on\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  if ($gt =~ /F1/) { print OUT "\tvisibility hide\n"; } else { print OUT "\tvisibility full\n"; }
  print OUT "\taggregate transparentOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:30:11\n";
  print OUT "\tpriority $prio\n\n";
  print OUT "\t\ttrack $mwtrack\Plus\n";
  print OUT "\t\tbigDataUrl DATA/$gt.mm9.methseqdepth.plus.bigwig\n";
  print OUT "\t\tshortLabel\t$gt WGBS depth, plus\n";
  print OUT "\t\tlongLabel\tWGBS depth (plus strand) for $gtLabels{$gt}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tgraphTypeDefault points\n";
  print OUT "\t\tcolor 0,0,255\n\n"; # dark blue
  print	OUT "\t\ttrack $mwtrack\Minus\n";
  print	OUT "\t\tbigDataUrl DATA/$gt.mm9.methseqdepth.minus.bigwig\n";
  print OUT "\t\tshortLabel\t$gt WGBS depth, minus\n";
  print	OUT "\t\tlongLabel\tWGBS depth (minus strand) for $gtLabels{$gt}\n";
  print	OUT "\t\tparent	$mwtrack\n";
  print	OUT "\t\ttype bigWig\n";
  print OUT "\t\tgraphTypeDefault points\n";
  print OUT "\t\tcolor 0,215,255\n\n"; # bright blue
}
print OUT "\n\n\n";



#CpG pctMeth by animal
$supertrack4_name = "st4_mpctCpG_ANI";
print OUT "track $supertrack4_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS CpG %Methylation by Animal\n";
print OUT "longLabel\tPercent methylation at cytosines in CpG context for each animal, per strand; validated and unvalidated sites are overlayed.  Data from WGBS.\n\n";
$pri=4.0;
foreach	$ani (@animals) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st4_$ani"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack4_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$ani CpG %methylation\n";
  print OUT "\tlongLabel\t$ani CpG %methylation\n";
  print OUT "\ttype bigWig -100 100\n";
  print OUT "\tviewLimits -100:100\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  print OUT "\tvisibility hide\n";
  print OUT "\taggregate solidOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:40:11\n";
  print OUT "\tpriority $prio\n\n";

  print OUT "\t\ttrack $mwtrack\VCpG\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CpG.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CpG %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CpG sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility full\n";
  print OUT "\t\tcolor 0,0,204\n\n";#blue
  print OUT "\t\ttrack $mwtrack\UCpG\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CpG.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CpG %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CpG sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility full\n";
  print OUT "\t\tcolor 204,0,0\n\n";#red
}
print OUT "\n\n\n";



#nonCpG pctMeth by animal
$supertrack5_name = "st5_mpctCHX_ANI";
print OUT "track $supertrack5_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS Non-CpG %Methylation by Animal\n";
print OUT "longLabel\tPercent methylation at cytosines in non-CpG context for each animal, per context, per strand; validated and unvalidated sites are overlayed.  Data from WGBS.\n\n";
$pri=5.0;
foreach $ani (@animals) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st5_$ani"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack5_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$ani non-CpG %methylation\n";
  print OUT "\tlongLabel\t$ani non-CpG %methylation\n";
  print OUT "\ttype bigWig -100 100\n";
  print OUT "\tviewLimits -100:100\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  print OUT "\tvisbility hide\n";
  print OUT "\taggregate solidOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:40:11\n";
  print OUT "\tpriority $prio\n\n";

  print OUT "\t\ttrack $mwtrack\VCHG\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CHG.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CHG %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CHG sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 153,51,204\n\n";#purple
  print OUT "\t\ttrack $mwtrack\UCHG\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CHG.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CHG %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CHG sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 255,102,0\n\n";#orange

  print OUT "\t\ttrack $mwtrack\VCHH\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CHH.mm9.methpct.validated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CHH %meth, val\n";
  print OUT "\t\tlongLabel\t%methylation at validated CHH sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 0,102,0\n\n";#darkgreen
  print OUT "\t\ttrack $mwtrack\UCHH\n";
  print OUT "\t\tbigDataUrl DATA/$ani.CHH.mm9.methpct.unvalidated.bigwig\n";
  print OUT "\t\tshortLabel\t$ani CHH %meth, unval\n";
  print OUT "\t\tlongLabel\t%methylation at unvalidated CHH sites for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tvisibility hide\n";
  print OUT "\t\tcolor 255,215,0\n\n";#darkyellow

}
print OUT "\n\n\n";



#depth by animal
$supertrack6_name = "st6_DepthANI";
print OUT "track $supertrack6_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS Depth by Animal\n";
print OUT "longLabel\tWGBS depth for each animal, per strand\n\n";
$pri = 6.0;
foreach $ani (@animals) {
  $pri+=0.1; $prio = sprintf("%.1f", $pri);
  $mwtrack = "st6_$ani"."_multiwig";
  print OUT "\ttrack $mwtrack\n";
  print OUT "\tparent $supertrack6_name\n";
  print OUT "\tcontainer multiWig\n";
  print OUT "\tshortLabel\t$ani WGBS depth\n";
  print OUT "\tlongLabel\t$ani WGBS depth\n";
  print OUT "\ttype bigWig\n";
  print OUT "\tviewLimits 0:100\n";
  print OUT "\twindowingFunction mean\n";
  print OUT "\tgridDefault on\n";
  print OUT "\tautoScale off\n";
  print OUT "\tconfigurable on\n";
  print OUT "\tvisibility hide\n";
  print OUT "\taggregate transparentOverlay\n";
  print OUT "\tshowSubtrackColorOnUi on\n";
  print OUT "\tmaxHeightPixels 150:30:11\n";
  print OUT "\tpriority $prio\n\n";
  print OUT "\t\ttrack $mwtrack\Plus\n";
  print OUT "\t\tbigDataUrl DATA/$ani.mm9.methseqdepth.plus.bigwig\n";
  print OUT "\t\tshortLabel\t$ani WGBS depth, plus\n";
  print OUT "\t\tlongLabel\tWGBS depth (plus strand) for $aniLabels{$ani}\n";
  print OUT "\t\tparent $mwtrack\n";
  print OUT "\t\ttype bigWig\n";
  print OUT "\t\tgraphTypeDefault points\n";
  print OUT "\t\tcolor 0,0,255\n\n"; # dark blue
  print	OUT "\t\ttrack $mwtrack\Minus\n";
  print	OUT "\t\tbigDataUrl DATA/$ani.mm9.methseqdepth.minus.bigwig\n";
  print OUT "\t\tshortLabel\t$ani WGBS depth, minus\n";
  print	OUT "\t\tlongLabel\tWGBS depth (minus strand) for $aniLabels{$ani}\n";
  print	OUT "\t\tparent	$mwtrack\n";
  print	OUT "\t\ttype bigWig\n";
  print OUT "\t\tgraphTypeDefault points\n";
  print OUT "\t\tcolor 0,215,255\n\n"; # bright blue
}
print OUT "\n\n\n";



#DMRs
@dmrRoots = ("B6-vs-C3","M-vs-F.B6+C3","M-vs-F.B6","M-vs-F.C3","M-vs-F.F1","mothers-vs-virgins");
%rootName = ("B6-vs-C3"=>"B6-vs-C3","M-vs-F.B6+C3"=>"M-vs-F.all","M-vs-F.B6"=>"M-vs-F.B6","M-vs-F.C3"=>"M-vs-F.C3","M-vs-F.F1"=>"M-vs-F.allF1","mothers-vs-virgins"=>"mothers-vs-virgins");
@dmrTools = ("DSS","Metilene");
$supertrack7_name = "st7_DMRs";
print OUT "track $supertrack7_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tDMRs\n";
print OUT "longLabel\tDMR tracks\n\n";
foreach $root (@dmrRoots) { foreach $tool (@dmrTools) {
  $bbfile = "$rootName{$root}.$tool.DMR.bigBed";
  print OUT "\ttrack $root.$tool.DMR\n";
  print OUT "\tparent $supertrack7_name\n";
  print OUT "\ttype bigBed 9\n";
  print OUT "\tshortLabel\t$root $tool DMRs\n";
  if ($root eq "B6-vs-C3") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, B6 vs C3 animals.\n"; }
  if ($root eq "M-vs-F.B6+C3") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, Male vs Female, parental animals.\n"; }
  if ($root eq "mothers-vs-virgins") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, Parental vs F1 female animals.\n"; }
  if ($root eq "M-vs-F.B6") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, Male vs Female, B6 animals\n"; }
  if ($root eq "M-vs-F.C3") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, Male vs Female, C3 animals\n"; }
  if ($root eq "M-vs-F.F1") { print OUT "\tlongLabel\tDifferentially methylated regions via $tool, Male vs Female, F1 animals\n"; }
  print OUT "\tbigDataUrl DATA/$bbfile\n";
  print OUT "\tvisibility dense\n";
  print OUT "\titemRgb on\n\n";
} }
print OUT "\n\n\n";




#reference info
$supertrack8_name = "st8_references";
print OUT "track $supertrack8_name\n";
print OUT "superTrack on show\n";
print OUT "shortLabel\tWGBS references\n";
print OUT "longLabel\tWGBS reference tracks\n\n";

print OUT "\ttrack SNVs\n";
print OUT "\tparent $supertrack8_name\n";
print OUT "\ttype bigBed 9\n";
print OUT "\tshortLabel\tSNVs in local genomes\n";
print OUT "\tlongLabel\tSNVs in local C57BL/6N and C3H/HeN genomes, relative to mm9. Differential sites [B6 vs C3] are red. Autosomes only.\n";
print OUT "\tbigDataUrl DATA/NISC_SNVs.mm9_canonAuto.bigBed\n";
print OUT "\tvisibility dense\n";
print OUT "\titemRgb on\n\n";

print OUT "\ttrack indels_B6\n";
print OUT "\tparent $supertrack8_name\n";
print OUT "\ttype bigBed 4\n";
print OUT "\tshortLabel\tB6 walkover indels\n";
print OUT "\tlongLabel\tInsertions/deletions in BL6 relative to mm9, from C57BL/6N assembly walkover.\n";
print OUT "\tbigDataUrl DATA/indel.mm9_vs_BL6.bigBed\n";
print OUT "\tvisibility	dense\n\n";

print OUT "\ttrack indels_C3\n";
print OUT "\tparent $supertrack8_name\n";
print OUT "\ttype bigBed 4\n";
print OUT "\tshortLabel\tC3 walkover indels\n";
print OUT "\tlongLabel\tInsertions/deletions in C3 relative to mm9, from C3H/HeN assembly walkover.\n";
print OUT "\tbigDataUrl DATA/indel.mm9_vs_C3H.bigBed\n";
print OUT "\tvisibility dense\n\n";


#FOXA1 ChIP-seq
$supertrack9_name = "st9_FOXA1chip"; ## actually, composite track not supertrack...
print OUT "track $supertrack9_name\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tFOXA1 ChIP-seq\n";
print OUT "longLabel\tFOXA1 ChIP-seq\n";
print OUT "priority\t9\n";
print OUT "visibility\tfull\n";
print OUT "view\tFOXA1COV\n";
print OUT "type\tbigWig\n";
print OUT "allButtonPair\ton\n";
print OUT "dragAndDrop\ton\n";
print OUT "alwaysZero\ton\n";
print OUT "graphTypeDefault\tbar\n";
print OUT "maxHeightPixels\t150:30:11\n";
print OUT "viewLimits\t0:65\n";
print OUT "showSubtrackColorOnUi\ton\n";
print OUT "viewUi\ton\n\n";
print OUT "windowingFunction mean\n";
print OUT "gridDefault on\n";
print OUT "autoScale off\n";
print OUT "configurable on\n";

print OUT "\t\ttrack B6.FOXA1.IP\n";
print OUT "\t\tbigDataUrl DATA/ChIP_FOXA1-B6-ds.bwt.rmdup.singlefrag.bigWig\n";
print OUT "\t\tshortLabel\tB6 FOXA1 IP\n";
print OUT "\t\tlongLabel\tB6 FOXA1 ChIP-seq, merged IP replicates\n";
print OUT "\t\tparent $supertrack9_name\n";
print OUT "\t\ttype bigWig\n";
#print OUT "\t\tgraphTypeDefault points\n";
print OUT "\t\tcolor 0,0,153\n\n"; # blue

print OUT "\t\ttrack C3.FOXA1.IP\n";
print OUT "\t\tbigDataUrl DATA/ChIP_FOXA1-C3-ds.bwt.rmdup.singlefrag.bigWig\n";
print OUT "\t\tshortLabel\tC3 FOXA1 IP\n";
print OUT "\t\tlongLabel\tC3 FOXA1 ChIP-seq, merged IP replicates\n";
print OUT "\t\tparent $supertrack9_name\n";
print OUT "\t\ttype bigWig\n";
#print OUT "\t\tgraphTypeDefault points\n";
print OUT "\t\tcolor 0,0,153\n\n"; # blue

print OUT "\t\ttrack B6.FOXA1.input\n";
print OUT "\t\tbigDataUrl DATA/input-B6-ds.bwt.rmdup.singlefrag.bigWig\n";
print OUT "\t\tshortLabel\tB6 FOXA1 input\n";
print OUT "\t\tlongLabel\tB6 FOXA1 ChIP-seq, merged input replicates\n";
print OUT "\t\tparent $supertrack9_name\n";
print OUT "\t\ttype bigWig\n";
#print OUT "\t\tgraphTypeDefault points\n";
print OUT "\t\tcolor 102,102,102\n\n"; # grey

print OUT "\t\ttrack C3.FOXA1.input\n";
print OUT "\t\tbigDataUrl DATA/input-C3-ds.bwt.rmdup.singlefrag.bigWig\n";
print OUT "\t\tshortLabel\tC3 FOXA1 input\n";
print OUT "\t\tlongLabel\tC3 FOXA1 ChIP-seq, merged input replicates\n";
print OUT "\t\tparent $supertrack9_name\n";
print OUT "\t\ttype bigWig\n";
#print OUT "\t\tgraphTypeDefault points\n";
print OUT "\t\tcolor 102,102,102\n\n"; # grey

print OUT "\n\n\n";


#print OUT "#\ttrack CpGislands\n";
#print OUT "#\tparent $supertrack8_name\n";
#print OUT "#\ttype bigBed 3\n";
#print OUT "#\tshortLabel\tCpG islands\n";
#print OUT "#\tlongLabel\tCpG islands as defined by CgiHunter (http://cgihunter.bioinf.mpi-inf.mpg.de/index.php)\n";
#print OUT "#\tbigDataUrl DATA/CpG-Island.mm9.bigBed\n";
#print OUT "#\tvisibility dense\n\n";

print OUT "\n\n\n";

close(OUT);