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Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites). 

Optimized Mapping Quality calculation.
 Correctly filtered reads below minimum Mapping Quality threshold
This commit is contained in:
Roger Zurawicki 2011-07-19 16:59:06 -04:00
parent d05d79218b 5493a4dd99
commit d92d00a85d
450 changed files with 2822 additions and 2131 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

60
build.xml
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@ -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
View File

@ -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
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@ -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
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@ -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
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@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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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