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Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-11 18:13:22 +00:00
parent 195b4ea7b4
commit 63b5c12cbd
57 changed files with 112 additions and 145 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceGenerationException.java → java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources;
package org.broadinstitute.sting.gatk.datasources;
import org.broadinstitute.sting.utils.StingException;

3
java/src/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
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@ -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;

13
java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java
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@ -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

4
java/src/org/broadinstitute/sting/gatk/dataSources/providers/InvalidPositionException.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java
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@ -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.

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -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;

6
java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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@ -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;

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
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@ -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;

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
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@ -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;

5
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java
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@ -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;

4
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceView.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
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@ -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;

8
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/dataSources/providers/View.java → java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java
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@ -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

5
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ExpGrowthLocusShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/ExpGrowthLocusShardStrategy.java
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@ -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
*

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShard.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShard.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java
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@ -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;

5
java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategy.java
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@ -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
*

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShard.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShard.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/LocusShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java
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@ -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;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShard.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadShardStrategy.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import net.sf.samtools.SAMSequenceDictionary;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/Shard.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategy.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.shards;
package org.broadinstitute.sting.gatk.datasources.shards;
import java.util.Iterator;
/**

2
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java → java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
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@ -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;

4
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataSource.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ResourcePool.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
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@ -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;

6
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
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@ -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;

4
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSource.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSource.java
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@ -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;

2
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceLoadException.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.StingException;

2
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java → java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;

2
java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
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@ -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;

4
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -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;

7
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -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;

14
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -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;
/**

4
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -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;

5
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -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;

8
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
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@ -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;

15
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -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;

12
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -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;

4
java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/AllLocusViewTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusViewTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewTest.java
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@ -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;

6
java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
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@ -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;

6
java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewTest.java
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@ -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;

8
java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedViewTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceViewTemplate.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProviderTest.java → java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java → java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java → java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java → java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java → java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceOrderedDataPoolTest.java → java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java
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@ -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;

9
java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java → java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java
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@ -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;

6
java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java → java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java
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@ -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;

10
java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java
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@ -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;

10
java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java
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@ -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;

4
java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java
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@ -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;