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
parent
1876c9856a
commit
7ad8fbdd5a
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@ -26,7 +26,7 @@
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package net.sf.picard.reference;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
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@ -1,7 +1,7 @@
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package org.broadinstitute.sting.alignment;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.Utils;
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
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import org.broadinstitute.sting.alignment.reference.bwt.BWT;
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.Alignment;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java;
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import org.broadinstitute.sting.alignment.Aligner;
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import org.broadinstitute.sting.alignment.Alignment;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.BaseUtils;
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import java.io.File;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.bwa.java;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.Deque;
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import java.util.ArrayDeque;
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@ -1,7 +1,7 @@
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package org.broadinstitute.sting.alignment.bwa.java;
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import org.broadinstitute.sting.alignment.Alignment;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import net.sf.samtools.Cigar;
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/**
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@ -1,7 +1,7 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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/**
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* Represents the Burrows-Wheeler Transform of a reference sequence.
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
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import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
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import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
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import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.*;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.HashMap;
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import java.util.Map;
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@ -31,7 +31,7 @@ import net.sf.picard.reference.ReferenceSequence;
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import java.io.*;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
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/**
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.Comparator;
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import java.util.TreeSet;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
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import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.bwt;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
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import java.io.*;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.packing;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.io.*;
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import java.nio.ByteOrder;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.packing;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.io.*;
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import java.nio.ByteBuffer;
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.alignment.reference.packing;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.io.File;
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import java.io.IOException;
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@ -25,7 +25,7 @@
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.List;
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import java.util.Collections;
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.Set;
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import java.util.HashSet;
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@ -24,7 +24,7 @@
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.lang.annotation.Annotation;
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.lang.reflect.Field;
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import java.util.Arrays;
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.gatk.walkers.Multiplex;
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import org.broadinstitute.sting.gatk.walkers.Multiplexer;
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.utils.Utils;
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@ -31,6 +31,7 @@ import net.sf.samtools.*;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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@ -30,7 +30,7 @@ import java.util.Map;
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import java.util.HashMap;
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import java.util.Collections;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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/**
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* Holds a bunch of basic information about the traversal.
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.gatk.filters.FilterManager;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.text.TextFormattingUtils;
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import org.broadinstitute.sting.utils.help.DescriptionTaglet;
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
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import net.sf.samtools.SAMFileReader;
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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package org.broadinstitute.sting.gatk.contexts;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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package org.broadinstitute.sting.gatk.contexts;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.BaseUtils;
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import net.sf.samtools.util.StringUtil;
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package org.broadinstitute.sting.gatk.contexts;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.pileup.*;
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@ -30,6 +30,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
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import org.broad.tribble.util.variantcontext.*;
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import org.broadinstitute.sting.utils.*;
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import org.broad.tribble.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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public class VariantContextUtils {
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package org.broadinstitute.sting.gatk.datasources;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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/**
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* User: aaron
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.gatk.datasources.providers;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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package org.broadinstitute.sting.gatk.datasources.providers;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.*;
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import java.util.Collections;
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@ -9,9 +8,9 @@ import java.util.Arrays;
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import net.sf.samtools.SAMSequenceRecord;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.util.StringUtil;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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/**
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* User: hanna
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* Date: May 22, 2009
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
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import org.broadinstitute.sting.gatk.datasources.shards.Shard;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import java.util.ArrayList;
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import java.util.List;
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@ -35,6 +35,7 @@ import java.util.*;
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import net.sf.samtools.*;
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import net.sf.picard.util.PeekableIterator;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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/**
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* Shard intervals based on position within the BAM file.
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@ -1,6 +1,6 @@
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package org.broadinstitute.sting.gatk.datasources.shards;
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import org.broadinstitute.sting.utils.GATKException;
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import org.broadinstitute.sting.utils.exceptions.GATKException;
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import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.gatk.ReadMetrics;
|
||||
import org.broadinstitute.sting.gatk.ReadProperties;
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ 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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
|
||||
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
|
||||
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.sam.CreateSequenceDictionary;
|
||||
import net.sf.picard.reference.IndexedFastaSequenceFile;
|
||||
|
|
|
|||
|
|
@ -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.walkers.ReadWalker;
|
||||
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.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
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.GenomeLocParser;
|
||||
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.ReadProperties;
|
|||
import org.broadinstitute.sting.gatk.ReadMetrics;
|
||||
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
|
||||
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 java.io.File;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
/**
|
||||
*
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
|
|||
|
||||
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
|
||||
/*
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ 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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.instrumentation.Sizeof;
|
||||
|
||||
import java.io.File;
|
||||
|
|
|
|||
|
|
@ -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.LocusShardDataProvider;
|
||||
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.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
|
||||
|
|
|
|||
|
|
@ -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.io.*;
|
||||
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 javax.management.MBeanServer;
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
|
|||
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.exceptions.GATKException;
|
||||
|
||||
import java.util.concurrent.Callable;
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
package org.broadinstitute.sting.gatk.executive;
|
||||
|
||||
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.Future;
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
|
||||
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.commandline.ArgumentSource;
|
||||
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
|
||||
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.utils.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.SAMFileWriterStub;
|
||||
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;
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ import org.broad.tribble.vcf.VCFHeader;
|
|||
import org.broad.tribble.vcf.VCFHeaderLine;
|
||||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
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 java.io.*;
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ import java.io.OutputStream;
|
|||
import org.broadinstitute.sting.gatk.io.OutputTracker;
|
||||
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
|
||||
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;
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ import java.util.Queue;
|
|||
import java.util.LinkedList;
|
||||
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
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
|
|||
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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.simpleframework.xml.Element;
|
||||
import org.simpleframework.xml.ElementList;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
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 java.io.File;
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
package org.broadinstitute.sting.gatk.refdata;
|
||||
|
||||
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.GenomeLocParser;
|
||||
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
|
||||
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.UserException;
|
||||
import org.broadinstitute.sting.utils.text.XReadLines;
|
||||
|
|
|
|||
|
|
@ -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.RODRecordList;
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
|
||||
import java.util.*;
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.LocationAwareSeekableRODIterator;
|
||||
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.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ import org.broad.tribble.Feature;
|
|||
import org.broadinstitute.sting.gatk.refdata.Transcript;
|
||||
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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@
|
|||
|
||||
package org.broadinstitute.sting.gatk.refdata.tracks;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ import org.broad.tribble.FeatureSource;
|
|||
import org.broad.tribble.source.BasicFeatureSource;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
|
||||
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.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.RMDTrack;
|
||||
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.classloader.PluginManager;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
|
|
|
|||
|
|
@ -30,10 +30,10 @@ import org.broad.tribble.vcf.VCFInfoHeaderLine;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
|
||||
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.walkers.annotator.interfaces.*;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.genotype.Haplotype;
|
||||
import org.broadinstitute.sting.utils.pileup.*;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.walkers.annotator.interfaces.*;
|
||||
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.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ import java.util.ArrayList;
|
|||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ import java.util.ArrayList;
|
|||
import java.util.Collections;
|
||||
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.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ 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.utils.BaseUtils;
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ import net.sf.samtools.SAMReadGroupRecord;
|
|||
import net.sf.samtools.SAMRecord;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
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.pileup.PileupElement;
|
||||
|
||||
|
|
|
|||
|
|
@ -40,6 +40,7 @@ import org.broadinstitute.sting.utils.*;
|
|||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
import java.io.File;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.fasta;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
import java.io.PrintStream;
|
||||
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
|
||||
package org.broadinstitute.sting.gatk.walkers.filters;
|
||||
|
||||
import org.broadinstitute.sting.utils.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
|
|
@ -82,7 +82,7 @@ public class FiltrationContextWindow {
|
|||
if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() )
|
||||
throw new GATKException("Too large a window requested");
|
||||
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];
|
||||
ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft);
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
|
|||
import org.broad.tribble.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
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.pileup.ReadBackedPileup;
|
||||
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
|
|||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.pileup.*;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.contexts.*;
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ import net.sf.samtools.util.SequenceUtil;
|
|||
import net.sf.picard.reference.IndexedFastaSequenceFile;
|
||||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.utils.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
|
||||
import org.broadinstitute.sting.utils.interval.IntervalUtils;
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
|
|||
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
|
||||
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
|
||||
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.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
|
|||
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.exceptions.GATKException;
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import net.sf.samtools.SAMFileWriter;
|
||||
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
|
|||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
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.pileup.ReadBackedPileup;
|
||||
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@
|
|||
|
||||
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.sam.GATKSAMRecord;
|
||||
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|||
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.exceptions.GATKException;
|
||||
|
||||
|
||||
@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
|
||||
|
|
|
|||
|
|
@ -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.DataPoint;
|
||||
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.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.DataPoint;
|
||||
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
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|||
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.exceptions.GATKException;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Arrays;
|
||||
|
|
|
|||
|
|
@ -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.DataPoint;
|
||||
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;
|
||||
|
||||
|
|
|
|||
|
|
@ -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.templates.ReportFormat;
|
||||
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.Utils;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
|
|
|
|||
|
|
@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
|
|||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
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.collections.ExpandingArrayList;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
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.exceptions.GATKException;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
|
||||
import java.io.PrintStream;
|
||||
|
|
|
|||
|
|
@ -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.utils.GATKFeature;
|
||||
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.GenomeLocParser;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
|
|
|
|||
|
|
@ -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.AlignmentContext;
|
||||
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.commandline.Argument;
|
||||
|
||||
|
|
|
|||
|
|
@ -21,6 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
|
|||
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
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.pileup.PileupElement;
|
||||
|
||||
|
|
|
|||
|
|
@ -28,7 +28,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
|
|||
import java.io.File;
|
||||
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.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
|
|||
import org.broadinstitute.sting.alignment.Alignment;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
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.GenomeLocParser;
|
||||
import net.sf.samtools.SAMRecord;
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue