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Moving StingException 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-09-12 14:34:15 +00:00
parent 8c16babe91
commit 595907e98e
112 changed files with 4 additions and 162 deletions
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1
java/src/org/broadinstitute/sting/alignment/Alignment.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;

1
java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
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@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;

2
java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java
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@ -1,7 +1,5 @@
package org.broadinstitute.sting.alignment.bwa;
import org.broadinstitute.sting.utils.StingException;
/**
* Configuration for the BWA/C aligner.
*

2
java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
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@ -1,8 +1,6 @@
package org.broadinstitute.sting.alignment.bwa;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
import org.broadinstitute.sting.alignment.reference.bwt.BWT;

1
java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.c;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;

1
java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.java;
import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File;

2
java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
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@ -1,8 +1,6 @@
package org.broadinstitute.sting.alignment.bwa.java;
import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.Deque;
import java.util.ArrayDeque;

4
java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
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@ -1,11 +1,7 @@
package org.broadinstitute.sting.alignment.bwa.java;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import net.sf.samtools.Cigar;
/**

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
* Represents the Burrows-Wheeler Transform of a reference sequence.

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.HashMap;
import java.util.Map;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
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@ -32,7 +32,6 @@ import net.sf.picard.reference.ReferenceSequence;
import java.io.*;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
/**

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.Comparator;
import java.util.TreeSet;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;

1
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
import java.io.*;

1
java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.nio.ByteOrder;

1
java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.nio.ByteBuffer;

1
java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;
import java.io.IOException;

1
java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import java.lang.annotation.Annotation;

1
java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.List;
import java.util.Collections;

1
java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.Set;
import java.util.HashSet;

1
java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.lang.annotation.Annotation;

2
java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
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@ -26,10 +26,8 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.lang.annotation.Annotation;
import java.util.Arrays;
import java.util.List;

2
java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
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@ -26,8 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.walkers.Walker;

6
java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -29,14 +29,8 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.gatk.walkers.Walker;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*;
import net.sf.picard.filter.SamRecordFilter;

1
java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
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@ -31,7 +31,6 @@ import java.util.HashMap;
import java.util.Collections;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
* Holds a bunch of basic information about the traversal.

1
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
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@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.help.DescriptionTaglet;
import org.broadinstitute.sting.utils.help.DisplayNameTaglet;

3
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.arguments;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
@ -77,7 +76,7 @@ public class GATKArgumentCollection {
@Element(required = false)
@Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? Standard is the default, can be verbose or NO_ET so nothing is posted to the run repository", required = false)
public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.NO_ET;
public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
@ElementList(required = false)
@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually.", required = false)

2
java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -28,10 +28,8 @@ package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import java.util.*;

1
java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import net.sf.samtools.util.StringUtil;

1
java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.datasources;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
* User: aaron

4
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -3,15 +3,11 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
import java.util.List;
/*
* Copyright (c) 2009 The Broad Institute
*

5
java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
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@ -1,11 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.StringUtil;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

1
java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.ArrayList;
import java.util.List;

1
java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties;

4
java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
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@ -1,16 +1,12 @@
package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.List;
import net.sf.samtools.SAMSequenceDictionary;
/**
* Create a giant shard representing all the data in the input BAM(s).
*

1
java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.shards;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;

1
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.List;

1
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
*

1
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/*

1
java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
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@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File;

1
java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
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@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.StingException;
import java.util.ArrayList;
import java.util.List;

2
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -8,9 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
import javax.management.MBeanServer;

1
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.concurrent.Callable;
/**

1
java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.concurrent.Callable;
import java.util.concurrent.Future;

2
java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import org.broadinstitute.sting.gatk.walkers.Walker;
@ -36,7 +35,6 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.OutputStreamStorage;
import java.io.*;
import java.lang.reflect.Field;

1
java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
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@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;

4
java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
View File

@ -26,16 +26,12 @@
package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import java.io.OutputStream;
import java.io.File;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Field;
/**
* Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.

2
java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
View File

@ -29,11 +29,9 @@ import net.sf.samtools.util.CloseableIterator;
import java.util.Queue;
import java.util.LinkedList;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
* Buffers access to a large stream of reads, replenishing the buffer only when the reads

3
java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
View File

@ -5,9 +5,6 @@ import net.sf.samtools.util.CloseableIterator;
import java.util.Iterator;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.utils.StingException;
/**
*
* User: aaron

1
java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
View File

@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.simpleframework.xml.Element;
import org.simpleframework.xml.ElementList;

2
java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
View File

@ -2,9 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import java.util.Iterator;
import java.io.File;
import java.io.IOException;

1
java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
View File

@ -4,7 +4,6 @@ import org.broad.tribble.util.variantcontext.Allele;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.util.*;

1
java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
View File

@ -4,7 +4,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;

1
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
View File

@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import java.util.ArrayList;
import java.util.List;

1
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.refdata.tracks;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**

1
java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.Comparator;

1
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.PrintStream;

1
java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;

1
java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
View File

@ -4,7 +4,6 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;

1
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
View File

@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")

1
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
View File

@ -8,7 +8,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/**
* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl

1
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
View File

@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.List;
import java.util.Arrays;

1
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
View File

@ -9,7 +9,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.ArrayList;

8
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -25,22 +25,14 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.io.PrintStream;
import java.util.*;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
View File

@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import java.io.PrintStream;
import java.util.*;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
View File

@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Output;
import java.util.*;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
View File

@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import java.util.ArrayList;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
View File

@ -13,7 +13,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.io.File;

1
java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
View File

@ -29,7 +29,6 @@ import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.PathUtils;
import org.broadinstitute.sting.playground.utils.ProcessUtils;

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
View File

@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.pileup.PileupElement;

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
View File

@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
View File

@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.ArrayList;
import java.util.List;

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
View File

@ -27,7 +27,6 @@ import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
public class BialleleSNP extends Biallele {

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
View File

@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.math.BigInteger;

1
java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
View File

@ -27,7 +27,6 @@ package org.broadinstitute.sting.playground.utils;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.StingException;
import org.apache.log4j.Logger;
/**

2
java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
View File

@ -27,11 +27,9 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.lang.annotation.Annotation;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;

1
java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
View File

@ -28,7 +28,6 @@ import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.lang.reflect.Field;

1
java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.playground.utils.report.templates.*;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import java.io.*;

2
java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java
View File

@ -1,7 +1,5 @@
package org.broadinstitute.sting.playground.utils.report.utils;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;
/**

1
java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescripto
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;
import java.io.IOException;

2
java/src/org/broadinstitute/sting/utils/GATKException.java
View File

@ -24,6 +24,8 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.utils.exceptions.StingException;
/**
* Temp class to track split from Sting exception to UserException
*/

2
java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.utils.classloader;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Modifier;
import java.lang.reflect.Field;
@ -34,7 +33,6 @@ import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Arrays;
/**

2
java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
View File

@ -27,9 +27,7 @@ package org.broadinstitute.sting.utils.classloader;
import ch.qos.logback.classic.Level;
import ch.qos.logback.classic.Logger;
import ch.qos.logback.classic.LoggerContext;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.reflections.Reflections;
import org.reflections.scanners.SubTypesScanner;

2
java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
View File

@ -26,8 +26,6 @@
package org.broadinstitute.sting.utils.classloader;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import java.util.HashMap;

1
java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.utils.collections;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/** This class, closely resembling a deque (except that it is not dynamically grown),

1
java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
View File

@ -29,7 +29,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import java.util.*;

1
java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.utils.fasta;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;

5
java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java
View File

@ -1,10 +1,5 @@
package org.broadinstitute.sting.utils.fastq;
import org.broadinstitute.sting.utils.StingException;
import java.io.BufferedReader;
import java.io.IOException;
public class FastqRecord {
private String seqHeader;
private String seqLine;

1
java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.file;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;
import java.io.IOException;

1
java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
View File

@ -4,7 +4,6 @@ import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.util.HashMap;

1
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
/*

1
java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
View File

@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils.help;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import java.util.List;

1
java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
View File

@ -32,7 +32,6 @@ import java.io.PrintStream;
import java.io.IOException;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.gatk.walkers.Walker;

1
java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.utils.instrumentation;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.StingException;
import java.lang.instrument.Instrumentation;
import java.lang.reflect.Field;

2
java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -24,10 +24,8 @@
package org.broadinstitute.sting.utils.pileup;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.gatk.iterators.IterableIterator;

1
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
View File

@ -25,7 +25,6 @@ package org.broadinstitute.sting.utils.pileup;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.*;

1
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -33,7 +33,6 @@ import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import java.util.ArrayList;

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