From a463dbcda170522e9719fe475dbd853b7790f9ae Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 19 Jan 2011 15:23:40 +0000
Subject: [PATCH] Refactoring the qscript directory; oneoffs, playground, and
 core

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5017 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/{ => oneoffs}/chartl/RefineGenotypesAndMerge.q      | 0
 scala/qscript/{ => oneoffs}/chartl/expanded_targets.q             | 0
 scala/qscript/{ => oneoffs}/chartl/fullCallingPipelineV2.q        | 0
 scala/qscript/{ => oneoffs}/chartl/old/private_mutations_old.q    | 0
 scala/qscript/{ => oneoffs}/chartl/omni_qc.q                      | 0
 scala/qscript/{ => oneoffs}/chartl/private_mutations.q            | 0
 scala/qscript/{ => oneoffs}/depristo/1kg_table1.scala             | 0
 scala/qscript/{ => oneoffs}/depristo/VQSRCutByNRS.scala           | 0
 .../qscript/{ => oneoffs}/depristo/manySampleUGPerformance.scala  | 0
 scala/qscript/{ => oneoffs}/depristo/phaseSamples.scala           | 0
 scala/qscript/{ => oneoffs}/depristo/resequencingSamples1KG.scala | 0
 scala/qscript/{ => oneoffs}/hanna/DoC.scala                       | 0
 scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.scala           | 0
 scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.sh              | 0
 scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.yaml            | 0
 .../kshakir/linearindexbintests/LinearIndexBinTests.scala         | 0
 .../kshakir/linearindexbintests/LinearIndexBinTests.sh            | 0
 .../qscript/{ => oneoffs}/kshakir/linearindexbintests/README.txt  | 0
 .../{ => oneoffs}/kshakir/linearindexbintests/grep_results.sh     | 0
 .../{ => oneoffs}/kshakir/linearindexbintests/plot_results.R      | 0
 scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/test_vcfs | 0
 scala/qscript/{ => oneoffs}/rpoplin/ASHGcalling.scala             | 0
 .../{ => oneoffs}/rpoplin/MethodsDevelopmentCallingPipeline.scala | 0
 scala/qscript/{ => oneoffs}/rpoplin/Phase1Calling.scala           | 0
 scala/qscript/{ => oneoffs}/rpoplin/Phase1Cleaning.scala          | 0
 scala/qscript/{ => oneoffs}/rpoplin/variantRecalibrator.scala     | 0
 .../{chartl/batchMergePipeline.q => playground/BatchMerge.q}      | 0
 scala/qscript/{ => playground}/fullCallingPipeline.q              | 0
 scala/qscript/{ => playground}/recalibrate.scala                  | 0
 29 files changed, 0 insertions(+), 0 deletions(-)
 rename scala/qscript/{ => oneoffs}/chartl/RefineGenotypesAndMerge.q (100%)
 rename scala/qscript/{ => oneoffs}/chartl/expanded_targets.q (100%)
 rename scala/qscript/{ => oneoffs}/chartl/fullCallingPipelineV2.q (100%)
 rename scala/qscript/{ => oneoffs}/chartl/old/private_mutations_old.q (100%)
 rename scala/qscript/{ => oneoffs}/chartl/omni_qc.q (100%)
 rename scala/qscript/{ => oneoffs}/chartl/private_mutations.q (100%)
 rename scala/qscript/{ => oneoffs}/depristo/1kg_table1.scala (100%)
 rename scala/qscript/{ => oneoffs}/depristo/VQSRCutByNRS.scala (100%)
 rename scala/qscript/{ => oneoffs}/depristo/manySampleUGPerformance.scala (100%)
 rename scala/qscript/{ => oneoffs}/depristo/phaseSamples.scala (100%)
 rename scala/qscript/{ => oneoffs}/depristo/resequencingSamples1KG.scala (100%)
 rename scala/qscript/{ => oneoffs}/hanna/DoC.scala (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.scala (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.sh (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/UGMemoryTests.yaml (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/LinearIndexBinTests.scala (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/LinearIndexBinTests.sh (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/README.txt (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/grep_results.sh (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/plot_results.R (100%)
 rename scala/qscript/{ => oneoffs}/kshakir/linearindexbintests/test_vcfs (100%)
 rename scala/qscript/{ => oneoffs}/rpoplin/ASHGcalling.scala (100%)
 rename scala/qscript/{ => oneoffs}/rpoplin/MethodsDevelopmentCallingPipeline.scala (100%)
 rename scala/qscript/{ => oneoffs}/rpoplin/Phase1Calling.scala (100%)
 rename scala/qscript/{ => oneoffs}/rpoplin/Phase1Cleaning.scala (100%)
 rename scala/qscript/{ => oneoffs}/rpoplin/variantRecalibrator.scala (100%)
 rename scala/qscript/{chartl/batchMergePipeline.q => playground/BatchMerge.q} (100%)
 rename scala/qscript/{ => playground}/fullCallingPipeline.q (100%)
 rename scala/qscript/{ => playground}/recalibrate.scala (100%)

diff --git a/scala/qscript/chartl/RefineGenotypesAndMerge.q b/scala/qscript/oneoffs/chartl/RefineGenotypesAndMerge.q
similarity index 100%
rename from scala/qscript/chartl/RefineGenotypesAndMerge.q
rename to scala/qscript/oneoffs/chartl/RefineGenotypesAndMerge.q
diff --git a/scala/qscript/chartl/expanded_targets.q b/scala/qscript/oneoffs/chartl/expanded_targets.q
similarity index 100%
rename from scala/qscript/chartl/expanded_targets.q
rename to scala/qscript/oneoffs/chartl/expanded_targets.q
diff --git a/scala/qscript/chartl/fullCallingPipelineV2.q b/scala/qscript/oneoffs/chartl/fullCallingPipelineV2.q
similarity index 100%
rename from scala/qscript/chartl/fullCallingPipelineV2.q
rename to scala/qscript/oneoffs/chartl/fullCallingPipelineV2.q
diff --git a/scala/qscript/chartl/old/private_mutations_old.q b/scala/qscript/oneoffs/chartl/old/private_mutations_old.q
similarity index 100%
rename from scala/qscript/chartl/old/private_mutations_old.q
rename to scala/qscript/oneoffs/chartl/old/private_mutations_old.q
diff --git a/scala/qscript/chartl/omni_qc.q b/scala/qscript/oneoffs/chartl/omni_qc.q
similarity index 100%
rename from scala/qscript/chartl/omni_qc.q
rename to scala/qscript/oneoffs/chartl/omni_qc.q
diff --git a/scala/qscript/chartl/private_mutations.q b/scala/qscript/oneoffs/chartl/private_mutations.q
similarity index 100%
rename from scala/qscript/chartl/private_mutations.q
rename to scala/qscript/oneoffs/chartl/private_mutations.q
diff --git a/scala/qscript/depristo/1kg_table1.scala b/scala/qscript/oneoffs/depristo/1kg_table1.scala
similarity index 100%
rename from scala/qscript/depristo/1kg_table1.scala
rename to scala/qscript/oneoffs/depristo/1kg_table1.scala
diff --git a/scala/qscript/depristo/VQSRCutByNRS.scala b/scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
similarity index 100%
rename from scala/qscript/depristo/VQSRCutByNRS.scala
rename to scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
diff --git a/scala/qscript/depristo/manySampleUGPerformance.scala b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
similarity index 100%
rename from scala/qscript/depristo/manySampleUGPerformance.scala
rename to scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
diff --git a/scala/qscript/depristo/phaseSamples.scala b/scala/qscript/oneoffs/depristo/phaseSamples.scala
similarity index 100%
rename from scala/qscript/depristo/phaseSamples.scala
rename to scala/qscript/oneoffs/depristo/phaseSamples.scala
diff --git a/scala/qscript/depristo/resequencingSamples1KG.scala b/scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
similarity index 100%
rename from scala/qscript/depristo/resequencingSamples1KG.scala
rename to scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
diff --git a/scala/qscript/hanna/DoC.scala b/scala/qscript/oneoffs/hanna/DoC.scala
similarity index 100%
rename from scala/qscript/hanna/DoC.scala
rename to scala/qscript/oneoffs/hanna/DoC.scala
diff --git a/scala/qscript/kshakir/UGMemoryTests.scala b/scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
similarity index 100%
rename from scala/qscript/kshakir/UGMemoryTests.scala
rename to scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
diff --git a/scala/qscript/kshakir/UGMemoryTests.sh b/scala/qscript/oneoffs/kshakir/UGMemoryTests.sh
similarity index 100%
rename from scala/qscript/kshakir/UGMemoryTests.sh
rename to scala/qscript/oneoffs/kshakir/UGMemoryTests.sh
diff --git a/scala/qscript/kshakir/UGMemoryTests.yaml b/scala/qscript/oneoffs/kshakir/UGMemoryTests.yaml
similarity index 100%
rename from scala/qscript/kshakir/UGMemoryTests.yaml
rename to scala/qscript/oneoffs/kshakir/UGMemoryTests.yaml
diff --git a/scala/qscript/kshakir/linearindexbintests/LinearIndexBinTests.scala b/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.scala
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/LinearIndexBinTests.scala
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.scala
diff --git a/scala/qscript/kshakir/linearindexbintests/LinearIndexBinTests.sh b/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.sh
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/LinearIndexBinTests.sh
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.sh
diff --git a/scala/qscript/kshakir/linearindexbintests/README.txt b/scala/qscript/oneoffs/kshakir/linearindexbintests/README.txt
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/README.txt
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/README.txt
diff --git a/scala/qscript/kshakir/linearindexbintests/grep_results.sh b/scala/qscript/oneoffs/kshakir/linearindexbintests/grep_results.sh
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/grep_results.sh
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/grep_results.sh
diff --git a/scala/qscript/kshakir/linearindexbintests/plot_results.R b/scala/qscript/oneoffs/kshakir/linearindexbintests/plot_results.R
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/plot_results.R
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/plot_results.R
diff --git a/scala/qscript/kshakir/linearindexbintests/test_vcfs b/scala/qscript/oneoffs/kshakir/linearindexbintests/test_vcfs
similarity index 100%
rename from scala/qscript/kshakir/linearindexbintests/test_vcfs
rename to scala/qscript/oneoffs/kshakir/linearindexbintests/test_vcfs
diff --git a/scala/qscript/rpoplin/ASHGcalling.scala b/scala/qscript/oneoffs/rpoplin/ASHGcalling.scala
similarity index 100%
rename from scala/qscript/rpoplin/ASHGcalling.scala
rename to scala/qscript/oneoffs/rpoplin/ASHGcalling.scala
diff --git a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
similarity index 100%
rename from scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
rename to scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
diff --git a/scala/qscript/rpoplin/Phase1Calling.scala b/scala/qscript/oneoffs/rpoplin/Phase1Calling.scala
similarity index 100%
rename from scala/qscript/rpoplin/Phase1Calling.scala
rename to scala/qscript/oneoffs/rpoplin/Phase1Calling.scala
diff --git a/scala/qscript/rpoplin/Phase1Cleaning.scala b/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
similarity index 100%
rename from scala/qscript/rpoplin/Phase1Cleaning.scala
rename to scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
diff --git a/scala/qscript/rpoplin/variantRecalibrator.scala b/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala
similarity index 100%
rename from scala/qscript/rpoplin/variantRecalibrator.scala
rename to scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala
diff --git a/scala/qscript/chartl/batchMergePipeline.q b/scala/qscript/playground/BatchMerge.q
similarity index 100%
rename from scala/qscript/chartl/batchMergePipeline.q
rename to scala/qscript/playground/BatchMerge.q
diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/playground/fullCallingPipeline.q
similarity index 100%
rename from scala/qscript/fullCallingPipeline.q
rename to scala/qscript/playground/fullCallingPipeline.q
diff --git a/scala/qscript/recalibrate.scala b/scala/qscript/playground/recalibrate.scala
similarity index 100%
rename from scala/qscript/recalibrate.scala
rename to scala/qscript/playground/recalibrate.scala