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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
David Roazen 2011-07-01 16:19:35 -04:00
parent d647ea4fdc b0fb63e20a
commit e9030a7bfd
7 changed files with 16 additions and 4 deletions
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8
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -41,9 +41,9 @@ class RecalibrateBaseQualities extends QScript {
nContigs = getNumberOfContigs(input)
val recalFile1: File = new File("recal1.csv")
val recalFile2: File = new File("recal2.csv")
val recalBam: File = swapExt(input, ".bam", "recal.bam")
val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
val recalBam: File = swapExt(input, ".bam", "recal.bam")
val path1: String = "before"
val path2: String = "after"
@ -88,4 +88,4 @@ class RecalibrateBaseQualities extends QScript {
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
}
}

2
public/scala/qscript/examples/ExampleCountLoci.scala → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

2
public/scala/qscript/examples/ExampleCountReads.scala → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

2
public/scala/qscript/examples/ExampleCustomWalker.scala → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

2
public/scala/qscript/examples/ExampleUnifiedGenotyper.scala → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._

2
public/scala/qscript/examples/HelloWorld.scala → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
class HelloWorld extends QScript {

2
public/scala/qscript/lib/Vcf2Table.q → public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q
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@ -1,3 +1,5 @@
package org.broadinstitute.sting.queue.qscripts.lib
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.queue.extensions.gatk.{RodBind, VariantsToTable}
import org.broadinstitute.sting.queue.QScript