From d19351f71acc60673286d5dc8b1e6516bcc7a4a3 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 1 Jul 2011 16:02:28 -0400 Subject: [PATCH 1/2] Added capability of running multiple bam files in the same directory. --- .../sting/queue/qscripts/RecalibrateBaseQualities.scala | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala index 678b356ee..51de3a7ad 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -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" } -} \ No newline at end of file +} From b0fb63e20a86e5d3542a1c5301663eb8cc884795 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 1 Jul 2011 16:14:59 -0400 Subject: [PATCH 2/2] moving the example scala scripts to the qscripts package. --- .../sting/queue/qscripts}/examples/ExampleCountLoci.scala | 2 ++ .../sting/queue/qscripts}/examples/ExampleCountReads.scala | 2 ++ .../sting/queue/qscripts}/examples/ExampleCustomWalker.scala | 2 ++ .../queue/qscripts}/examples/ExampleUnifiedGenotyper.scala | 2 ++ .../sting/queue/qscripts}/examples/HelloWorld.scala | 2 ++ .../broadinstitute/sting/queue/qscripts}/lib/Vcf2Table.q | 2 ++ 6 files changed, 12 insertions(+) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCountLoci.scala (93%) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCountReads.scala (97%) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCustomWalker.scala (96%) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleUnifiedGenotyper.scala (98%) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/HelloWorld.scala (76%) rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/lib/Vcf2Table.q (95%) diff --git a/public/scala/qscript/examples/ExampleCountLoci.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala similarity index 93% rename from public/scala/qscript/examples/ExampleCountLoci.scala rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala index ba834e72f..4ca3cbb89 100644 --- a/public/scala/qscript/examples/ExampleCountLoci.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala @@ -1,3 +1,5 @@ +package org.broadinstitute.sting.queue.qscripts.examples + import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ diff --git a/public/scala/qscript/examples/ExampleCountReads.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala similarity index 97% rename from public/scala/qscript/examples/ExampleCountReads.scala rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala index 85f796a51..9fdd1ba4c 100644 --- a/public/scala/qscript/examples/ExampleCountReads.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala @@ -1,3 +1,5 @@ +package org.broadinstitute.sting.queue.qscripts.examples + import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ diff --git a/public/scala/qscript/examples/ExampleCustomWalker.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala similarity index 96% rename from public/scala/qscript/examples/ExampleCustomWalker.scala rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala index 340934b5b..d3796d350 100644 --- a/public/scala/qscript/examples/ExampleCustomWalker.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala @@ -1,3 +1,5 @@ +package org.broadinstitute.sting.queue.qscripts.examples + import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ diff --git a/public/scala/qscript/examples/ExampleUnifiedGenotyper.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala similarity index 98% rename from public/scala/qscript/examples/ExampleUnifiedGenotyper.scala rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala index 2f6940d64..4a93233eb 100644 --- a/public/scala/qscript/examples/ExampleUnifiedGenotyper.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala @@ -1,3 +1,5 @@ +package org.broadinstitute.sting.queue.qscripts.examples + import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ diff --git a/public/scala/qscript/examples/HelloWorld.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala similarity index 76% rename from public/scala/qscript/examples/HelloWorld.scala rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala index 64e0c161c..9f2ce27fe 100644 --- a/public/scala/qscript/examples/HelloWorld.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala @@ -1,3 +1,5 @@ +package org.broadinstitute.sting.queue.qscripts.examples + import org.broadinstitute.sting.queue.QScript class HelloWorld extends QScript { diff --git a/public/scala/qscript/lib/Vcf2Table.q b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q similarity index 95% rename from public/scala/qscript/lib/Vcf2Table.q rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q index 1b66a648b..25ff8fddd 100755 --- a/public/scala/qscript/lib/Vcf2Table.q +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q @@ -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