From 3d134a84975b2dabec377142a9c3d6a651879006 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 25 May 2011 02:14:55 +0000 Subject: [PATCH] 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 --- scala/qscript/core/GATKResourcesBundle.scala | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/scala/qscript/core/GATKResourcesBundle.scala b/scala/qscript/core/GATKResourcesBundle.scala index e8b100ecb..d37206c68 100755 --- a/scala/qscript/core/GATKResourcesBundle.scala +++ b/scala/qscript/core/GATKResourcesBundle.scala @@ -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)) //