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
2011-01-19 15:23:40 +00:00 · 2011-01-19 15:23:40 +00:00 · a463dbcda1
parent 24bc843ae8
commit a463dbcda1
29 changed files with 0 additions and 0 deletions
--- a/scala/qscript/oneoffs/chartl/RefineGenotypesAndMerge.q
+++ b/scala/qscript/oneoffs/chartl/RefineGenotypesAndMerge.q
--- a/scala/qscript/oneoffs/chartl/expanded_targets.q
+++ b/scala/qscript/oneoffs/chartl/expanded_targets.q
--- a/scala/qscript/oneoffs/chartl/fullCallingPipelineV2.q
+++ b/scala/qscript/oneoffs/chartl/fullCallingPipelineV2.q
--- a/scala/qscript/oneoffs/chartl/old/private_mutations_old.q
+++ b/scala/qscript/oneoffs/chartl/old/private_mutations_old.q
--- a/scala/qscript/oneoffs/chartl/omni_qc.q
+++ b/scala/qscript/oneoffs/chartl/omni_qc.q
--- a/scala/qscript/oneoffs/chartl/private_mutations.q
+++ b/scala/qscript/oneoffs/chartl/private_mutations.q
--- a/scala/qscript/oneoffs/depristo/1kg_table1.scala
+++ b/scala/qscript/oneoffs/depristo/1kg_table1.scala
--- a/scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
+++ b/scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
--- a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
+++ b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
--- a/scala/qscript/oneoffs/depristo/phaseSamples.scala
+++ b/scala/qscript/oneoffs/depristo/phaseSamples.scala
--- a/scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
+++ b/scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
--- a/scala/qscript/oneoffs/hanna/DoC.scala
+++ b/scala/qscript/oneoffs/hanna/DoC.scala
--- a/scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
+++ b/scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
--- a/scala/qscript/oneoffs/kshakir/UGMemoryTests.sh
+++ b/scala/qscript/oneoffs/kshakir/UGMemoryTests.sh
--- a/scala/qscript/oneoffs/kshakir/UGMemoryTests.yaml
+++ b/scala/qscript/oneoffs/kshakir/UGMemoryTests.yaml
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.scala
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.scala
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.sh
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.sh
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/README.txt
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/README.txt
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/grep_results.sh
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/grep_results.sh
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/plot_results.R
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/plot_results.R
--- a/scala/qscript/oneoffs/kshakir/linearindexbintests/test_vcfs
+++ b/scala/qscript/oneoffs/kshakir/linearindexbintests/test_vcfs
--- a/scala/qscript/oneoffs/rpoplin/ASHGcalling.scala
+++ b/scala/qscript/oneoffs/rpoplin/ASHGcalling.scala
--- a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
+++ b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
--- a/scala/qscript/oneoffs/rpoplin/Phase1Calling.scala
+++ b/scala/qscript/oneoffs/rpoplin/Phase1Calling.scala
--- a/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
+++ b/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
--- a/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala
+++ b/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala
--- a/scala/qscript/chartl/batchMergePipeline.q
+++ b/scala/qscript/chartl/batchMergePipeline.q
--- a/scala/qscript/playground/fullCallingPipeline.q
+++ b/scala/qscript/playground/fullCallingPipeline.q
--- a/scala/qscript/playground/recalibrate.scala
+++ b/scala/qscript/playground/recalibrate.scala