diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceGenerationException.java b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java similarity index 94% rename from java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceGenerationException.java rename to java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java index 945629097..e18347d67 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceGenerationException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources; +package org.broadinstitute.sting.gatk.datasources; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java index 7574caa23..f6391b926 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java @@ -1,9 +1,8 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import java.util.NoSuchElementException; import java.util.ArrayList; -import org.broadinstitute.sting.gatk.iterators.LocusIterator; import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java similarity index 72% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java index ee7cd7d21..d9d4b365c 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java @@ -1,19 +1,8 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.gatk.iterators.LocusContextIterator; -import org.broadinstitute.sting.gatk.iterators.LocusContextIteratorByHanger; import org.broadinstitute.sting.gatk.LocusContext; -import org.broadinstitute.sting.gatk.Reads; -import org.broadinstitute.sting.gatk.traversals.TraversalEngine; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; import org.broadinstitute.sting.utils.GenomeLoc; import org.apache.log4j.Logger; -import net.sf.samtools.SAMRecord; - -import java.util.ArrayList; -import java.util.Iterator; - -import net.sf.picard.filter.FilteringIterator; /** * User: hanna * Date: May 12, 2009 diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/InvalidPositionException.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java similarity index 82% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/InvalidPositionException.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java index 801f90780..2e41a01b4 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/InvalidPositionException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java @@ -1,6 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; - -import org.broadinstitute.sting.utils.StingException; +package org.broadinstitute.sting.gatk.datasources.providers; /** * Created by IntelliJ IDEA. diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java similarity index 97% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index f32879b53..a8a7232ca 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.utils.GenomeLoc; import net.sf.picard.reference.ReferenceSequence; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java similarity index 97% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index 456a45576..49b805fcd 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -1,18 +1,16 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.Reads; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.iterators.LocusContextIteratorByHanger; import org.broadinstitute.sting.gatk.iterators.LocusContextIterator; import org.broadinstitute.sting.gatk.traversals.TraversalStatistics; -import org.broadinstitute.sting.utils.GenomeLoc; import net.sf.samtools.SAMRecord; import java.util.Iterator; import java.util.NoSuchElementException; import java.util.Collection; -import java.util.Collections; import java.util.Arrays; import net.sf.picard.filter.FilteringIterator; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java index 172e1767b..a683e2941 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceRecord; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java index 86e90e3a4..3b8bdf301 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java similarity index 93% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java index 4ba75b5be..c9e2a0263 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java @@ -1,9 +1,8 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RODIterator; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java similarity index 88% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceView.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java index 813d3c76a..367dd204c 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java @@ -1,7 +1,5 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.StingException; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import java.util.Collections; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java similarity index 95% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java index ec949b269..486a8e8b6 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java @@ -1,10 +1,10 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.NullSAMIterator; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; import org.broadinstitute.sting.gatk.Reads; import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/View.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java similarity index 90% rename from java/src/org/broadinstitute/sting/gatk/dataSources/providers/View.java rename to java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java index 10f3e21d4..18c6d357c 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/View.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java @@ -1,6 +1,5 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; -import java.util.List; import java.util.Collection; /** * User: hanna diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ExpGrowthLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ExpGrowthLocusShardStrategy.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ExpGrowthLocusShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/ExpGrowthLocusShardStrategy.java index 611659181..03634aba8 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ExpGrowthLocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ExpGrowthLocusShardStrategy.java @@ -1,11 +1,8 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import java.util.List; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShard.java similarity index 97% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShard.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShard.java index 7530cb672..5e08fe1e5 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShard.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java index 42d24b83b..fbb6159fc 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategy.java similarity index 95% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategy.java index f84c89d8b..3e858ead4 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategy.java @@ -1,11 +1,8 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import java.util.List; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShard.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShard.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShard.java index af0143810..d993016d5 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShard.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java similarity index 99% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java index 851ad172b..3f18c1d4c 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShard.java similarity index 97% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShard.java index 677f00d33..413dc27a7 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShard.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShardStrategy.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShardStrategy.java index b29e26c8e..9d5d0bb83 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShardStrategy.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/Shard.java similarity index 94% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/Shard.java index bed3ffae1..c4ad2600d 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/Shard.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategy.java similarity index 94% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategy.java index dd7908e0b..8a57e57bf 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategy.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import java.util.Iterator; /** diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java rename to java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java index 5fadafb0e..3a771e719 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataSource.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java index c76d6c537..b20638b3e 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java @@ -1,9 +1,9 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.RODIterator; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.Iterator; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ResourcePool.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ResourcePool.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java index 12d93d24b..5a8b0c75a 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ResourcePool.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java @@ -1,8 +1,7 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.StingException; -import org.apache.log4j.Logger; import java.util.List; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index c0ff97eba..b3085a523 100755 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import net.sf.picard.sam.SamFileHeaderMerger; import net.sf.picard.util.PeekableIterator; @@ -8,8 +8,8 @@ import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.CloseableIterator; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.dataSources.shards.ReadShard; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ReadShard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.Reads; import org.broadinstitute.sting.gatk.traversals.TraversalEngine; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSource.java similarity index 88% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSource.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSource.java index fa27680b7..af15f6eac 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSource.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import java.io.Serializable; import java.util.Iterator; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceLoadException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java similarity index 93% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceLoadException.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java index 0b84b7c9a..0eda44bf4 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceLoadException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java rename to java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java index b38553730..79fbea0f6 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java index f8243f378..2fec7ac59 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Pair; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index c2ad28011..d903a2b4e 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.OutputTracker; import org.broadinstitute.sting.gatk.Reads; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 5032d5a52..42250cf67 100644 --- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -1,13 +1,12 @@ package org.broadinstitute.sting.gatk.executive; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.Reads; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 414ec123c..ddf418fba 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -2,12 +2,12 @@ package org.broadinstitute.sting.gatk.executive; import net.sf.picard.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.traversals.TraverseReads; import org.broadinstitute.sting.gatk.traversals.TraverseLoci; @@ -26,8 +26,6 @@ import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import java.io.File; import java.io.FileNotFoundException; import java.util.List; -import java.util.Map; -import java.util.HashMap; import java.util.ArrayList; /** diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 2d517513a..d6bd6fc1d 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.executive; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.OutputTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 159df73ca..8a162f6a7 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.traversals; import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.filter.FilteringIterator; import net.sf.picard.reference.ReferenceSequence; -import net.sf.picard.sam.SamFileHeaderMerger; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader.ValidationStringency; @@ -13,8 +12,8 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.Reads; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2; diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java index 50266bb09..4360e70be 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java @@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.traversals; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.LocusContext; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.providers.ReadView; -import org.broadinstitute.sting.gatk.dataSources.shards.ReadShard; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ReadView; +import org.broadinstitute.sting.gatk.datasources.shards.ReadShard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 13e953d04..79abd003e 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -5,14 +5,13 @@ import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.providers.AllLocusView; -import org.broadinstitute.sting.gatk.dataSources.providers.CoveredLocusView; -import org.broadinstitute.sting.gatk.dataSources.providers.LocusView; -import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceOrderedView; -import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceView; -import org.broadinstitute.sting.gatk.dataSources.providers.LocusReferenceView; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.AllLocusView; +import org.broadinstitute.sting.gatk.datasources.providers.CoveredLocusView; +import org.broadinstitute.sting.gatk.datasources.providers.LocusView; +import org.broadinstitute.sting.gatk.datasources.providers.ReferenceOrderedView; +import org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index f6046058a..c3642d360 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -3,12 +3,12 @@ package org.broadinstitute.sting.gatk.traversals; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.LocusContext; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.providers.ReadView; -import org.broadinstitute.sting.gatk.dataSources.providers.ReadReferenceView; -import org.broadinstitute.sting.gatk.dataSources.shards.ReadShard; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.IntervalShard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ReadView; +import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView; +import org.broadinstitute.sting.gatk.datasources.shards.ReadShard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.IntervalShard; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.ReadWalker; diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java index 1fb3a41bd..0622a50f8 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java @@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.traversals.TraversalStatistics; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.LocusContext; import org.apache.log4j.Logger; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewTest.java similarity index 96% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusViewTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewTest.java index a86a7e327..56c630153 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.Assert; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusViewTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewTest.java index 043c96cff..3b3fcb525 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.Assert; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java similarity index 93% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java index 1f33702ee..48563d5f8 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java @@ -1,10 +1,10 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.Test; import org.junit.Assert; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.LocusShard; import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; import net.sf.picard.reference.ReferenceSequence; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java index 042fd030c..d173ad899 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java @@ -1,12 +1,12 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.BeforeClass; import org.junit.Test; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.LocusShard; import org.broadinstitute.sting.gatk.Reads; import java.io.FileNotFoundException; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewTest.java index aafca4350..3a811249d 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.utils.GenomeLoc; import org.junit.Assert; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java similarity index 95% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedViewTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java index 8c718f19c..a0a01ce9e 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedViewTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.Test; import org.junit.BeforeClass; @@ -8,9 +8,9 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.TabularROD; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.LocusShard; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.BaseTest; import java.io.File; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceViewTemplate.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceViewTemplate.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java index 54c254633..dbf2050a3 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceViewTemplate.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProviderTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderTest.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProviderTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderTest.java index 192a38643..437912d1c 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProviderTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.providers; +package org.broadinstitute.sting.gatk.datasources.providers; import org.junit.Before; import org.junit.Assert; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java index 1f0bc2932..ed18bfd9c 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.junit.Test; import org.junit.Before; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardTest.java index a703e7c4a..9e2779cff 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java index 23d6da164..c1eafd637 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryTest.java similarity index 98% rename from java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryTest.java index 85ca15add..3283f328b 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.shards; +package org.broadinstitute.sting.gatk.datasources.shards; import static junit.framework.Assert.assertEquals; import static junit.framework.Assert.fail; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataPoolTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java similarity index 99% rename from java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataPoolTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java index 5f174ab7b..d078758ae 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataPoolTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import org.junit.Before; import org.junit.BeforeClass; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java similarity index 95% rename from java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java index e0d44c9c3..589ee054a 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java @@ -1,12 +1,11 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import static junit.framework.Assert.fail; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; -import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.Reads; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java rename to java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java index f10ef2b27..e73d70ec5 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java @@ -1,11 +1,11 @@ -package org.broadinstitute.sting.gatk.dataSources.simpleDataSources; +package org.broadinstitute.sting.gatk.datasources.simpleDataSources; import static junit.framework.Assert.fail; import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory; import org.broadinstitute.sting.gatk.iterators.BoundedReadIterator; import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.Reads; diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java index 1c55ff5d5..da6bce391 100755 --- a/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java +++ b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java @@ -3,11 +3,11 @@ package org.broadinstitute.sting.gatk.iterators; import static junit.framework.Assert.fail; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SimpleDataSourceLoadException; import org.broadinstitute.sting.gatk.Reads; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2; diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java index 4e9707e98..aaaa89c94 100755 --- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.gatk.traversals; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; -import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; -import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory; +import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.CountReadsWalker; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java index 53dc5a3d7..152fabb3f 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.dataSources.shards.Shard; -import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.shards.Shard; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal; import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;