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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-22 14:42:04 -04:00
parent f50145b872 4080e2cd88
commit 4f78025b0b
1 changed files with 10 additions and 4 deletions
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14
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -15,8 +15,8 @@ class GATKResourcesBundle extends QScript {
@Argument(doc="liftOverPerl", required=false)
var liftOverPerl: File = new File("./perl/liftOverVCF.pl")
@Argument(shortName = "svn", doc="The SVN version of this release", required=true)
var SVN_VERSION: String = _
@Argument(shortName = "ver", doc="The SVN version of this release", required=true)
var VERSION: String = _
@Argument(shortName = "bundleDir", doc="Path to root where resource files will be placed", required=false)
val BUNDLE_ROOT = new File("/humgen/gsa-hpprojects/GATK/bundle")
@ -32,8 +32,8 @@ class GATKResourcesBundle extends QScript {
val SITES_EXT: String = "sites"
def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + SVN_VERSION
def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + SVN_VERSION
def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + VERSION
def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + VERSION
// REFERENCES
class Reference( val name: String, val file: File ) { }
@ -113,6 +113,12 @@ class GATKResourcesBundle extends QScript {
addResource(new Resource(hg19.file, "", hg19, false))
addResource(new Resource(hg18.file, "", hg18, false))
//
// The b37_decoy reference
//
addResource(new Resource("/humgen/1kg/reference/human_g1k_v37_decoy.fasta",
"IGNORE", b37, false, false))
//
// standard VCF files. Will be lifted to each reference
//