From efd99c3c117e2a423c93e9390076d1b9437d406b Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 30 Jun 2011 11:32:06 -0400
Subject: [PATCH] new home for the core qscripts

---
 .../sting/queue/qscripts}/DataProcessingPipeline.scala          | 2 +-
 .../sting/queue/qscripts}/GATKResourcesBundle.scala             | 2 +-
 .../queue/qscripts}/MethodsDevelopmentCallingPipeline.scala     | 2 ++
 .../sting/queue/qscripts}/RecalibrateBaseQualities.scala        | 2 +-
 .../sting/queue/qscripts}/StandardVariantEvaluation.scala       | 2 +-
 5 files changed, 6 insertions(+), 4 deletions(-)
 rename public/scala/qscript/{core => org/broadinstitute/sting/queue/qscripts}/DataProcessingPipeline.scala (99%)
 rename public/scala/qscript/{core => org/broadinstitute/sting/queue/qscripts}/GATKResourcesBundle.scala (99%)
 rename public/scala/qscript/{core => org/broadinstitute/sting/queue/qscripts}/MethodsDevelopmentCallingPipeline.scala (99%)
 rename public/scala/qscript/{core => org/broadinstitute/sting/queue/qscripts}/RecalibrateBaseQualities.scala (98%)
 rename public/scala/qscript/{core => org/broadinstitute/sting/queue/qscripts}/StandardVariantEvaluation.scala (99%)

diff --git a/public/scala/qscript/core/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
similarity index 99%
rename from public/scala/qscript/core/DataProcessingPipeline.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index cad19bd23..fdde5e8a2 100755
--- a/public/scala/qscript/core/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -1,4 +1,4 @@
-package core
+package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
diff --git a/public/scala/qscript/core/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
similarity index 99%
rename from public/scala/qscript/core/GATKResourcesBundle.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 24ae045d3..150d78019 100755
--- a/public/scala/qscript/core/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -1,4 +1,4 @@
-package core
+package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
diff --git a/public/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
similarity index 99%
rename from public/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index 632c03499..d71c6ae5d 100755
--- a/public/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts
+
 import org.broadinstitute.sting.commandline.Hidden
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
diff --git a/public/scala/qscript/core/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
similarity index 98%
rename from public/scala/qscript/core/RecalibrateBaseQualities.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index ba13d267a..678b356ee 100755
--- a/public/scala/qscript/core/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -1,4 +1,4 @@
-package core
+package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
diff --git a/public/scala/qscript/core/StandardVariantEvaluation.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/StandardVariantEvaluation.scala
similarity index 99%
rename from public/scala/qscript/core/StandardVariantEvaluation.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/StandardVariantEvaluation.scala
index d6af7019e..d333e1dc0 100755
--- a/public/scala/qscript/core/StandardVariantEvaluation.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/StandardVariantEvaluation.scala
@@ -1,4 +1,4 @@
-package core
+package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk.RodBind