fix packages

broadinstitute · Jan 30, 2018 · ac93a3b · ac93a3b
1 parent 186c08c
commit ac93a3b
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/...ctionaryValidationArgumentCollection.java → ...ctionaryValidationArgumentCollection.java b/...ctionaryValidationArgumentCollection.java → ...ctionaryValidationArgumentCollection.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.hellbender.engine.spark;
+package org.broadinstitute.hellbender.cmdline.argumentcollections;
 
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java b/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
@@ -21,7 +21,7 @@
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;
 import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
-import org.broadinstitute.hellbender.engine.spark.SequenceDictionaryValidationArgumentCollection;
+import org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.transformers.ReadTransformer;
 import org.broadinstitute.hellbender.utils.SequenceDictionaryUtils;

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSpark.java
@@ -8,7 +8,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
-import org.broadinstitute.hellbender.engine.spark.SequenceDictionaryValidationArgumentCollection;
+import org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;

diff --git a/...rg/broadinstitute/hellbender/tools/spark/pipelines/BwaAndMarkDuplicatesPipelineSpark.java b/...rg/broadinstitute/hellbender/tools/spark/pipelines/BwaAndMarkDuplicatesPipelineSpark.java
@@ -8,7 +8,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
-import org.broadinstitute.hellbender.engine.spark.SequenceDictionaryValidationArgumentCollection;
+import org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.spark.GATKSparkTool;

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java
@@ -18,7 +18,6 @@
 import org.broadinstitute.hellbender.engine.spark.AddContextDataToReadSpark;
 import org.broadinstitute.hellbender.engine.spark.GATKSparkTool;
 import org.broadinstitute.hellbender.engine.spark.JoinStrategy;
-import org.broadinstitute.hellbender.engine.spark.SequenceDictionaryValidationArgumentCollection;
 import org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection;

diff --git a/...naryValidationArgumentCollectionTest.java → ...naryValidationArgumentCollectionTest.java b/...naryValidationArgumentCollectionTest.java → ...naryValidationArgumentCollectionTest.java
@@ -1,9 +1,10 @@
-package org.broadinstitute.hellbender.engine.spark;
+package org.broadinstitute.hellbender.cmdline.argumentcollections;
 
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
 import org.broadinstitute.barclay.argparser.CommandLineArgumentParser;
 import org.broadinstitute.barclay.argparser.CommandLineParser;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection;
 import org.testng.Assert;
 import org.testng.annotations.Test;