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gatk-3.8
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Moved GATKException to exceptions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-09-12 14:47:19 +00:00
parent 1876c9856a
commit 7ad8fbdd5a
160 changed files with 164 additions and 139 deletions
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2
java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
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@ -26,7 +26,7 @@
package net.sf.picard.reference; package net.sf.picard.reference;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*; import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;

2
java/src/org/broadinstitute/sting/alignment/Alignment.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.alignment; package org.broadinstitute.sting.alignment;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;

2
java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;

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

2
java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles; import org.broadinstitute.sting.alignment.bwa.BWTFiles;

2
java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java;
import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File; import java.io.File;

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

2
java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.alignment.bwa.java; package org.broadinstitute.sting.alignment.bwa.java;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import net.sf.samtools.Cigar; import net.sf.samtools.Cigar;
/** /**

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

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.alignment.reference.packing.PackUtils;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.*; import java.util.*;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
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@ -31,7 +31,7 @@ import net.sf.picard.reference.ReferenceSequence;
import java.io.*; import java.io.*;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
/** /**

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.Comparator; import java.util.Comparator;
import java.util.TreeSet; import java.util.TreeSet;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.alignment.reference.packing.PackUtils;

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.bwt; package org.broadinstitute.sting.alignment.reference.bwt;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
import java.io.*; import java.io.*;

2
java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing; package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.io.*; import java.io.*;
import java.nio.ByteOrder; import java.nio.ByteOrder;

2
java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing; package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.io.*; import java.io.*;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;

2
java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.alignment.reference.packing; package org.broadinstitute.sting.alignment.reference.packing;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;

2
java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.List; import java.util.List;
import java.util.Collections; import java.util.Collections;

2
java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.Set; import java.util.Set;
import java.util.HashSet; import java.util.HashSet;

2
java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
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@ -24,7 +24,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.lang.annotation.Annotation; import java.lang.annotation.Annotation;

2
java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.lang.reflect.Field; import java.lang.reflect.Field;
import java.util.Arrays; import java.util.Arrays;

2
java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplex;
import org.broadinstitute.sting.gatk.walkers.Multiplexer; import org.broadinstitute.sting.gatk.walkers.Multiplexer;

2
java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;

2
java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;

1
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -31,6 +31,7 @@ import net.sf.samtools.*;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;

2
java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
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@ -30,7 +30,7 @@ import java.util.Map;
import java.util.HashMap; import java.util.HashMap;
import java.util.Collections; import java.util.Collections;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* Holds a bunch of basic information about the traversal. * Holds a bunch of basic information about the traversal.

2
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.help.DescriptionTaglet; import org.broadinstitute.sting.utils.help.DescriptionTaglet;

2
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;

2
java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -26,7 +26,7 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

2
java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.StringUtil;

2
java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.pileup.*;

1
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -30,6 +30,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broad.tribble.util.variantcontext.*; import org.broad.tribble.util.variantcontext.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broad.tribble.vcf.VCFConstants; import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
public class VariantContextUtils { public class VariantContextUtils {

2
java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.datasources; package org.broadinstitute.sting.gatk.datasources;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* User: aaron * User: aaron

2
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;

3
java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import java.util.Collections; import java.util.Collections;
@ -9,9 +8,9 @@ import java.util.Arrays;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.StringUtil;
import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* User: hanna * User: hanna
* Date: May 22, 2009 * Date: May 22, 2009

2
java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;

1
java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
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@ -35,6 +35,7 @@ import java.util.*;
import net.sf.samtools.*; import net.sf.samtools.*;
import net.sf.picard.util.PeekableIterator; import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* Shard intervals based on position within the BAM file. * Shard intervals based on position within the BAM file.

2
java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.shards; package org.broadinstitute.sting.gatk.datasources.shards;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;

2
java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.datasources.simpleDataSources; package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import net.sf.picard.reference.FastaSequenceIndexBuilder; import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.sam.CreateSequenceDictionary; import net.sf.picard.sam.CreateSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
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@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.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.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
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@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File; import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.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.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* *

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/* /*

2
java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof; import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File; import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;

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

2
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.concurrent.Callable; import java.util.concurrent.Callable;
/** /**

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

2
java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.io; package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.commandline.ArgumentSource; import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;

2
java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.io.storage; package org.broadinstitute.sting.gatk.io.storage;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.io.File; import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -5,7 +5,7 @@ import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine; import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFWriter; import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import java.io.*; import java.io.*;

2
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
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@ -35,7 +35,7 @@ import java.io.OutputStream;
import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
/** /**

2
java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
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@ -31,7 +31,7 @@ import java.util.Queue;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* Buffers access to a large stream of reads, replenishing the buffer only when the reads * Buffers access to a large stream of reads, replenishing the buffer only when the reads

2
java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.simpleframework.xml.Element; import org.simpleframework.xml.Element;
import org.simpleframework.xml.ElementList; import org.simpleframework.xml.ElementList;

2
java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.File; import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Allele;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

2
java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;

2
java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.*; import java.util.*;

2
java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
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@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
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@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
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@ -4,7 +4,7 @@ import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.Transcript; import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
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@ -23,7 +23,7 @@
package org.broadinstitute.sting.gatk.refdata.tracks; package org.broadinstitute.sting.gatk.refdata.tracks;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java
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@ -30,7 +30,7 @@ import org.broad.tribble.FeatureSource;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -36,7 +36,7 @@ import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.analyzeannotations; package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.Comparator; import java.util.Comparator;

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -30,10 +30,10 @@ import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.genotype.Haplotype; import org.broadinstitute.sting.utils.genotype.Haplotype;
import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.pileup.*;

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -49,7 +49,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*; import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
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@ -33,7 +33,7 @@ import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
/** /**

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
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@ -31,7 +31,7 @@ import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
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@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
/** /**

2
java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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@ -4,7 +4,7 @@ import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;

1
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -40,6 +40,7 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File; import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.fasta; package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.io.PrintStream; import java.io.PrintStream;

4
java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.filters; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.*; import java.util.*;
@ -82,7 +82,7 @@ public class FiltrationContextWindow {
if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() ) if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() )
throw new GATKException("Too large a window requested"); throw new GATKException("Too large a window requested");
if ( elementsToLeft < 0 || elementsToRight < 0 ) if ( elementsToLeft < 0 || elementsToRight < 0 )
throw new GATKException("Window size cannot be negative"); throw new GATKException("Window size cannot be negative");
FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1]; FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1];
ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft); ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft);

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
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@ -30,6 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.vcf.VCFConstants; import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
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@ -5,6 +5,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.*;

1
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -31,6 +31,7 @@ import net.sf.samtools.util.SequenceUtil;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;

2
java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.collections.PrimitivePair;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;

2
java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriter;

1
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

1
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration; package org.broadinstitute.sting.gatk.walkers.recalibration;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
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@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample") @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
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@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
/** /**
* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.List; import java.util.List;
import java.util.Arrays; import java.util.Arrays;

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import java.util.ArrayList; import java.util.ArrayList;

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -45,7 +45,7 @@ import org.broadinstitute.sting.playground.utils.report.ReportMarshaller;
import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory; import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory;
import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.utils.Node; import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
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@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
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@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.PrintStream; import java.io.PrintStream;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
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@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.features.samread.SAMReadFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
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@ -21,6 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.GATKException; import org.broadinstitute.sting.utils.exceptions.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;

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