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Fixed import conflict

This commit is contained in:
Menachem Fromer 2011-07-18 13:23:20 -04:00
parent d8ba4ab835 5493a4dd99
commit 4adead3099
441 changed files with 2565 additions and 1962 deletions
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60
build.xml
View File

@ -780,6 +780,50 @@
</sequential>
</macrodef>
<!-- FAILED-TEST -->
<macrodef name="run-failed-test">
<attribute name="xmlfailedtestfile" />
<sequential>
<!-- Get the pipeline run type. Default to dry. -->
<condition property="pipeline.run" value="dry" else="${pipeline.run}">
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
</condition>
<condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
<isset property="include.contracts" />
</condition>
<mkdir dir="${report}/failed_rerun" />
<echo message="Sting: Running @{xmlfailedtestfile} test cases!"/>
<taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
<testng outputDir="${report}/failed_rerun"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
workingDir="${basedir}"
useDefaultListeners="false"
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
<jvmarg value="-Xmx${test.maxmemory}" />
<jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
</classpath>
<xmlfileset dir="${basedir}" includes="@{xmlfailedtestfile}" />
</testng>
<fail message="test failed" if="test.failure" />
</sequential>
</macrodef>
<!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
<target name="test" depends="test.compile,tribble.test" description="Run unit tests">
@ -814,6 +858,22 @@
<run-test testtype="${pipetype}"/>
</target>
<target name="failed-test" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*UnitTest/testng-failed.xml" />
</target>
<target name="failed-integration" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*IntegrationTest/testng-failed.xml" />
</target>
<target name="failed-performance" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*PerformanceTest/testng-failed.xml" />
</target>
<target name="failed-pipeline" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
</target>
<!-- ***************************************************************************** -->
<!-- *********** Tribble ********* -->
<!-- ***************************************************************************** -->

11
public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -25,20 +25,21 @@
package org.broadinstitute.sting.analyzecovariates;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.walkers.recalibration.*;
import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import java.io.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import java.io.*;
/**
* Created by IntelliJ IDEA.

7
public/java/src/org/broadinstitute/sting/commandline/Argument.java
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@ -25,12 +25,7 @@
package org.broadinstitute.sting.commandline;
import java.lang.annotation.Documented;
import java.lang.annotation.ElementType;
import java.lang.annotation.Inherited;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.lang.annotation.*;
/**
* Created by IntelliJ IDEA.

4
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
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@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.List;
import java.util.Collections;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/**
* A group of argument definitions.

4
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
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@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Set;
import java.util.HashSet;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
/**
* A collection of argument definitions.

6
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -25,12 +25,12 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.walkers.Multiplex;
import org.broadinstitute.sting.gatk.walkers.Multiplexer;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.lang.annotation.Annotation;

10
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -25,14 +25,20 @@
package org.broadinstitute.sting.commandline;
import org.apache.log4j.*;
import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import java.io.IOException;
import java.util.*;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Locale;
public abstract class CommandLineProgram {

10
public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
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@ -25,11 +25,17 @@
package org.broadinstitute.sting.commandline;
import org.apache.log4j.*;
import org.apache.log4j.Appender;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
import java.lang.annotation.Annotation;
import java.util.Collections;
import java.util.Enumeration;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* Static utility methods for working with command-line arguments.

2
public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
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@ -26,8 +26,6 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils;
import java.util.Collection;
/**
* Specifies that a value was missing when attempting to populate an argument.
*/

10
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
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@ -25,16 +25,16 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import org.apache.log4j.Logger;
import java.lang.reflect.*;
import java.lang.reflect.Field;
import java.util.*;
/**

4
public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
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@ -27,10 +27,8 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
import java.util.List;
import java.util.ArrayList;
import java.util.regex.Pattern;
/**
* Holds a pattern, along with how to get to the argument definitions that could match that pattern.

21
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -25,30 +25,21 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.Walker;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
import net.sf.picard.filter.SamRecordFilter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.ListFileUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
/**
* @author aaron

10
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -26,13 +26,15 @@
package org.broadinstitute.sting.gatk;
import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.Attribution;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;

15
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -28,24 +28,14 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.*;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.ArgumentException;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reads.*;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.MonolithicShardStrategy;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
@ -65,6 +55,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.util.*;

9
public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
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@ -25,13 +25,12 @@
package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter;
import java.util.Map;
import java.util.HashMap;
import java.util.Collections;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/**
* Holds a bunch of basic information about the traversal.
*/

1
public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;

7
public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
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@ -25,19 +25,18 @@
package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DescriptionTaglet;
import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
import org.broadinstitute.sting.utils.help.SummaryTaglet;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;

11
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -26,17 +26,16 @@
package org.broadinstitute.sting.gatk.arguments;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.simpleframework.xml.*;
import org.simpleframework.xml.core.Persister;
import org.simpleframework.xml.stream.Format;

6
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -26,13 +26,13 @@
package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*;
import java.util.List;
/**
* Useful class for forwarding on locusContext data from this iterator

2
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
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@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.*;

9
public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -25,11 +25,12 @@
package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.BaseUtils;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.util.StringUtil;
import com.google.java.contract.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
/**
* The section of the reference that overlaps with the given

16
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
View File

@ -1,16 +1,14 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import java.util.Collections;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.ArrayList;
import java.util.Collections;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
/**
* User: hanna
* Date: May 13, 2009

11
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -1,13 +1,12 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/*
* Copyright (c) 2009 The Broad Institute
*

9
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
View File

@ -1,16 +1,15 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocParser;
/**
* Presents data sharded by locus to the traversal engine.
*

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
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@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
/**
* User: hanna
* Date: May 21, 2009

3
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
View File

@ -1,9 +1,8 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
/*
* Copyright (c) 2009 The Broad Institute
*

7
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
View File

@ -1,14 +1,13 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocParser;
/**
* Present data sharded by read to a traversal engine.
*

5
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
View File

@ -1,11 +1,10 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import java.util.Collection;
import java.util.Arrays;
import net.sf.samtools.SAMRecord;
import java.util.Collection;
/**
* User: hanna
* Date: May 22, 2009

18
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
View File

@ -1,16 +1,16 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.*;
import java.util.Collections;
import java.util.Collection;
import java.util.Arrays;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMRecord;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
/**
* User: hanna
* Date: May 22, 2009

4
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
View File

@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;

5
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
View File

@ -1,15 +1,14 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
import java.util.List;
import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import java.util.List;
/**
* User: hanna
* Date: May 8, 2009

5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
View File

@ -24,9 +24,6 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.File;
@ -35,9 +32,7 @@ import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Created by IntelliJ IDEA.

7
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
View File

@ -39,12 +39,7 @@ import java.io.RandomAccessFile;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
* Writes schedules for a single BAM file to a target output file.

12
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
View File

@ -26,20 +26,10 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.GATKBAMFileSpan;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.*;
/**
* Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once.

10
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
View File

@ -29,19 +29,11 @@ import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.SAMFileSpan;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeMap;
import java.util.*;
/**
* Represents a small section of a BAM file, and every associated interval.

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
View File

@ -23,24 +23,18 @@
*/
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.Bin;
import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.GATKBin;
import net.sf.samtools.GATKChunk;
import net.sf.samtools.LinearIndex;
import net.sf.samtools.SAMException;
import net.sf.samtools.util.RuntimeIOException;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.lang.ref.SoftReference;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* A basic interface for querying BAM indices.

6
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
View File

@ -24,11 +24,7 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.Bin;
import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.GATKBin;
import net.sf.samtools.GATKChunk;
import net.sf.samtools.LinearIndex;
import net.sf.samtools.*;
import java.util.ArrayList;
import java.util.Collections;

11
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
View File

@ -35,16 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.PriorityQueue;
import java.util.Queue;
import java.util.*;
/**
* Shard intervals based on position within the BAM file.

3
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
View File

@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
@ -7,8 +8,6 @@ import org.broadinstitute.sting.utils.Utils;
import java.util.List;
import java.util.Map;
import net.sf.samtools.SAMFileSpan;
/**
* Handles locus shards of BAM information.
* @author aaron

17
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
View File

@ -24,17 +24,18 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.GATKBAMFileSpan;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.util.*;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMFileSpan;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* A sharding strategy for loci based on reading of the index.

2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
View File

@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
View File

@ -4,8 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.List;
import java.util.NoSuchElementException;
/**
* Create a giant shard representing all the data in the input BAM(s).

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
View File

@ -1,15 +1,17 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
import java.util.*;
import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
/**
*
* User: aaron

5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
View File

@ -25,12 +25,11 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan;
import java.util.*;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.util.*;
/**
* The sharding strategy for reads using a simple counting mechanism. Each read shard
* has a specific number of reads (default to 10K) which is configured in the constructor.

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -24,21 +24,19 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.sam.MergingSamRecordIterator;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.picard.sam.MergingSamRecordIterator;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ;

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
View File

@ -2,17 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.Serializable;
import java.util.Collections;
import java.util.List;
import java.util.Map;

4
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
View File

@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/**
*

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
View File

@ -25,17 +25,17 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import net.sf.samtools.BAMIndex;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File;
import java.lang.reflect.Field;
import java.util.Map;
import java.util.List;
import net.sf.samtools.*;
import java.util.Map;
/**
*

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
View File

@ -24,12 +24,12 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import java.io.File;

1
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;

11
public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
View File

@ -25,16 +25,15 @@
package org.broadinstitute.sting.gatk.datasources.reference;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.sam.CreateSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.FastaSequenceIndex;
import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.sam.CreateSequenceDictionary;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.file.FSLockWithShared;
import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import java.io.File;

6
public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
View File

@ -28,11 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
* A pool of open resources, all of which can create a closeable iterator.

5
public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
View File

@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.datasources.sample;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.yaml.snakeyaml.TypeDescription;
import org.yaml.snakeyaml.Yaml;
import org.yaml.snakeyaml.constructor.Constructor;

17
public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
View File

@ -1,15 +1,20 @@
package org.broadinstitute.sting.gatk.examples;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.utils.pileup.*;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
/**
* Computes the coverage per sample.

4
public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
View File

@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.examples;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -32,8 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;

12
public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
View File

@ -25,18 +25,18 @@
package org.broadinstitute.sting.gatk.executive;
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.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
import java.util.List;
import java.util.Iterator;
import java.util.List;
/**
* Manages the
*/

18
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -1,27 +1,27 @@
package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
import java.util.Queue;
import java.util.LinkedList;
import java.util.Collection;
import java.util.concurrent.Executors;
import java.util.LinkedList;
import java.util.Queue;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.FutureTask;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/**
* A microscheduler that schedules shards according to a tree-like structure.
* Requires a special walker tagged with a 'TreeReducible' interface.

11
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -1,22 +1,21 @@
package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/** A micro-scheduling manager for single-threaded execution of a traversal. */
public class LinearMicroScheduler extends MicroScheduler {

25
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -25,26 +25,18 @@
package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.ReadMetrics;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.util.*;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.threading.*;
@ -52,6 +44,11 @@ import org.broadinstitute.sting.utils.threading.*;
import javax.management.JMException;
import javax.management.MBeanServer;
import javax.management.ObjectName;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.util.Collection;
/**

3
public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
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@ -1,10 +1,9 @@
package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import java.util.Collection;
import java.util.ArrayList;
import java.util.Collection;
/**
* User: hanna

4
public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
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@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.executive;
import java.util.Queue;
import java.util.List;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Queue;
import java.util.concurrent.Future;
/**
* User: hanna

6
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -1,13 +1,13 @@
package org.broadinstitute.sting.gatk.executive;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
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.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.concurrent.Callable;

2
public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
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@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.concurrent.Callable;
import java.util.concurrent.Future;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
/**
* User: hanna
* Date: Apr 29, 2009

19
public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
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@ -1,17 +1,20 @@
package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.*;
import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import java.util.*;
import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
/**
* Buffer shards of data which may or may not contain multiple loci into
* iterators of all data which cover an interval. Its existence is an homage

6
public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
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@ -24,8 +24,10 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.*;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
/**
* Filter out reads with wonky cigar strings.

1
public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**

13
public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
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@ -23,17 +23,16 @@
*/
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.util.CloserUtil;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Collection;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.util.CloserUtil;
import org.broadinstitute.sting.gatk.ReadMetrics;
import java.util.Collection;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
* Filtering Iterator which takes a filter and an iterator and iterates
* through only those records which are not rejected by the filter.

1
public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/*

1
public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**

3
public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
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@ -25,11 +25,8 @@
package org.broadinstitute.sting.gatk.filters;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import net.sf.picard.filter.SamRecordFilter;
import java.util.Collection;
/**

2
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
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@ -24,8 +24,8 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.util.QualityUtil;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.QualityUtils;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**

1
public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/*

1
public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**

2
public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
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@ -25,9 +25,7 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**

4
public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
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@ -25,11 +25,9 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**
* Filter out PL matching reads.

10
public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
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@ -1,14 +1,12 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import java.util.Set;
import java.util.HashSet;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.HashSet;
import java.util.Set;
/**
* Created by IntelliJ IDEA.
* User: asivache

1
public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
/**

13
public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
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@ -25,17 +25,16 @@
package org.broadinstitute.sting.gatk.filters;
import java.util.*;
import java.util.Map.Entry;
import java.io.File;
import java.io.FileNotFoundException;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
import java.util.Map.Entry;
/**
* Removes records matching the read group tag and exact match string.
* For example, this filter value:

1
public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;

3
public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
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@ -25,9 +25,8 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import java.util.Set;

3
public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
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@ -25,9 +25,8 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
/**

1
public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**

4
public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
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@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
/**
* Maps creation of storage directly to output streams in parent.

16
public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
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@ -26,20 +26,20 @@
package org.broadinstitute.sting.gatk.io;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import java.io.*;
import java.io.OutputStream;
import java.lang.reflect.Field;
import java.util.Map;
import java.util.HashMap;
import java.util.Map;
/**
* Manages the output and err streams that are created specifically for walker

2
public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.io;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
/**
* A writer that will allow unsorted BAM files to be written

9
public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
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@ -25,15 +25,16 @@
package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.executive.OutputMergeTask;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.*;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
/**
* An output tracker that can either track its output per-thread or directly,

4
public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
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@ -25,14 +25,14 @@
package org.broadinstitute.sting.gatk.io.storage;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.channels.WritableByteChannel;
import java.nio.channels.Channels;
public class OutputStreamStorage extends OutputStream implements Storage<OutputStream> {
/**

9
public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -27,17 +27,16 @@ package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
import java.io.*;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter;
import java.io.File;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
/**
* Provides temporary storage for SAMFileWriters.
*

2
public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
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@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.io.storage;
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.Stub;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

19
public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -1,16 +1,21 @@
package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.apache.log4j.Logger;
import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import java.io.*;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintStream;
/**
* Provides temporary and permanent storage for genotypes in VCF format.

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
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@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.OutputStream;
import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
/**

4
public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
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@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import java.io.OutputStream;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
/**
* A stub for routing and management of anything backed by an OutputStream.

8
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
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@ -24,14 +24,14 @@
package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.commandline.ArgumentSource;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.ArgumentMatches;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import net.sf.samtools.SAMFileReader;
import java.io.File;

9
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -25,18 +25,17 @@
package org.broadinstitute.sting.gatk.io.stubs;
import net.sf.samtools.SAMFileWriter;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import net.sf.samtools.SAMFileWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.lang.annotation.Annotation;
import java.util.List;
import java.util.Arrays;
import java.io.File;
import java.io.OutputStream;
import java.lang.annotation.Annotation;
import java.util.Arrays;
import java.util.List;
/**
* Insert a SAMFileWriterStub instead of a full-fledged concrete OutputStream implementations.

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