Move to barclay

Author: tomwhite

src/main/java/org/broadinstitute/hellbender/engine/spark/AssemblyRegionWalkerSpark.java

@@ -6,8 +6,8 @@
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.broadcast.Broadcast;
-import org.broadinstitute.hellbender.cmdline.Advanced;
-import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.barclay.argparser.Advanced;
+import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;

src/main/java/org/broadinstitute/hellbender/engine/spark/GATKSparkTool.java

@@ -1,11 +1,5 @@
 package org.broadinstitute.hellbender.engine.spark;
 
-import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKCommandLinePluginDescriptor;
-import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
-import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
-import org.broadinstitute.hellbender.engine.FeatureDataSource;
-import org.broadinstitute.hellbender.engine.FeatureManager;
-import org.broadinstitute.hellbender.utils.SerializableFunction;
 import com.google.cloud.genomics.dataflow.utils.GCSOptions;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -19,6 +13,8 @@
 import org.broadinstitute.hellbender.cmdline.argumentcollections.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceWindowFunctions;
+import org.broadinstitute.hellbender.engine.FeatureDataSource;
+import org.broadinstitute.hellbender.engine.FeatureManager;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
 import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink;

src/main/java/org/broadinstitute/hellbender/engine/spark/IntervalWalkerSpark.java

@@ -4,7 +4,7 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.broadcast.Broadcast;
-import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
 import org.broadinstitute.hellbender.utils.IntervalUtils;

src/main/java/org/broadinstitute/hellbender/engine/spark/LocusWalkerSpark.java

@@ -12,7 +12,6 @@
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
-import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator;

src/main/java/org/broadinstitute/hellbender/engine/spark/ReadWalkerSpark.java

@@ -5,7 +5,7 @@
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.broadcast.Broadcast;
-import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
 import org.broadinstitute.hellbender.utils.IntervalUtils;

src/main/java/org/broadinstitute/hellbender/engine/spark/VariantWalkerSpark.java

@@ -7,7 +7,7 @@
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.broadcast.Broadcast;
-import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerSpark.java

@@ -4,8 +4,8 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.Function;
-import org.broadinstitute.hellbender.cmdline.Argument;
-import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.programgroups.ReadProgramGroup;
 import org.broadinstitute.hellbender.engine.*;

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerSpark.java

@@ -4,9 +4,9 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.Function;
-import org.broadinstitute.hellbender.cmdline.Argument;
-import org.broadinstitute.hellbender.cmdline.ArgumentCollection;
-import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.ArgumentCollection;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection;
 import org.broadinstitute.hellbender.cmdline.programgroups.IntervalProgramGroup;

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceSpark.java

@@ -3,8 +3,8 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.Function;
-import org.broadinstitute.hellbender.cmdline.Argument;
-import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.programgroups.ReadProgramGroup;
 import org.broadinstitute.hellbender.engine.ReferenceContext;

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerSpark.java

@@ -4,8 +4,8 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.Function;
-import org.broadinstitute.hellbender.cmdline.Argument;
-import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;
 import org.broadinstitute.hellbender.engine.*;