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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) //Console.printf("liftover(%s => %s)%n", inRef.name, outRef.name)
(inRef.name, outRef.name) match { (inRef.name, outRef.name) match {
case ("b37", "hg19") => 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") => case ("b37", "hg18") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37tohg18.chain"), inRef, outRef) return new LiftOverPerl(in, out, new File("chainFiles/b37tohg18.chain"), inRef, outRef)
case ("b37", "b36") => case ("b37", "b36") =>
@ -100,14 +100,16 @@ class GATKResourcesBundle extends QScript {
// //
// references // 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")) 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")) 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")) b36 = new Reference("b36", new File("/humgen/1kg/reference/human_b36_both.fasta"))
exampleFASTA = new Reference("exampleFASTA", new File("testdata/exampleFASTA.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(b37.file, "", b37, false))
addResource(new Resource(b36.file, "", b36, false)) addResource(new Resource(b36.file, "", b36, false))
addResource(new Resource(hg19.file, "", hg19, false))
addResource(new Resource(hg18.file, "", hg18, false)) addResource(new Resource(hg18.file, "", hg18, false))
// //