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Updated to produce (actual) hg19 resources too 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5870 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-05-25 02:14:55 +00:00
parent 389c546757
commit 3d134a8497
1 changed files with 4 additions and 2 deletions
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6
scala/qscript/core/GATKResourcesBundle.scala
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@ -56,7 +56,7 @@ class GATKResourcesBundle extends QScript {
//Console.printf("liftover(%s => %s)%n", inRef.name, outRef.name)
(inRef.name, outRef.name) match {
case ("b37", "hg19") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37Tohg19.chain"), inRef, outRef)
return new LiftOverPerl(in, out, new File("chainFiles/b37tohg19.chain"), inRef, outRef)
case ("b37", "hg18") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37tohg18.chain"), inRef, outRef)
case ("b37", "b36") =>
@ -100,14 +100,16 @@ class GATKResourcesBundle extends QScript {
//
// references
//
hg19 = new Reference("hg19", new File("/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta"))
b37 = new Reference("b37", new File("/humgen/1kg/reference/human_g1k_v37.fasta"))
hg18 = new Reference("hg18", new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"))
b36 = new Reference("b36", new File("/humgen/1kg/reference/human_b36_both.fasta"))
exampleFASTA = new Reference("exampleFASTA", new File("testdata/exampleFASTA.fasta"))
refs = List(b37, hg18, b36, exampleFASTA)
refs = List(hg19, b37, hg18, b36, exampleFASTA)
addResource(new Resource(b37.file, "", b37, false))
addResource(new Resource(b36.file, "", b36, false))
addResource(new Resource(hg19.file, "", hg19, false))
addResource(new Resource(hg18.file, "", hg18, false))
//