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Removed the "Walker" suffix from all walkers that had it. 

* Did not touch archived walkers... those can be named whatever.
   * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
   * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
This commit is contained in:
Mauricio Carneiro 2012-07-20 16:33:29 -04:00
parent dea049553a
commit 116885a450
115 changed files with 1807 additions and 576 deletions
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3
ivy.xml
View File

@ -100,6 +100,9 @@
<!-- MongoDB for the GXDB project -->
<dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
<!-- GSON for talking to the REST API on Vanilla Forums -->
<dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
<exclude org="javax.servlet" />
<exclude org="javax.jms" />

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
View File

@ -40,7 +40,7 @@ import java.util.Map;
*/
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
public class CompareBAMWalker extends LocusWalker<Map<CompareBAMWalker.TestName, Boolean>, CompareBAMWalker.TestResults> {
public class CompareBAM extends LocusWalker<Map<CompareBAM.TestName, Boolean>, CompareBAM.TestResults> {
@Argument(required = true, shortName = "rr", fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID;
@Argument(required = false, shortName = "teq", fullName = "test_equal_bases", doc = "Test if the bases marked as '=' are indeed ref bases.") public boolean TEST_EQUAL_BASES = false;
@Argument(required = false, shortName = "tbc", fullName = "test_base_counts", doc = "Test if the base counts tag in consensus reads are accurate.") public boolean TEST_BASE_COUNTS = false;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
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@ -53,7 +53,7 @@ public class MultiSampleCompressor implements Compressor {
final double minAltProportionToTriggerVariant,
final double minIndelProportionToTriggerVariant,
final int minBaseQual,
final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) {
final ReduceReads.DownsampleStrategy downsampleStrategy) {
for ( String name : SampleUtils.getSAMFileSamples(header) ) {
compressorsPerSample.put(name,
new SingleSampleCompressor(name, contextSize, downsampleCoverage,

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -83,7 +83,7 @@ import java.util.*;
@PartitionBy(PartitionType.INTERVAL)
@ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class})
public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceReadsStash> {
public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceReadsStash> {
@Output
protected StingSAMFileWriter out;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
View File

@ -26,7 +26,7 @@ public class SingleSampleCompressor implements Compressor {
protected double minIndelProportionToTriggerVariant;
protected int minBaseQual;
protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy;
protected ReduceReads.DownsampleStrategy downsampleStrategy;
public SingleSampleCompressor(final String sampleName,
final int contextSize,
@ -35,7 +35,7 @@ public class SingleSampleCompressor implements Compressor {
final double minAltProportionToTriggerVariant,
final double minIndelProportionToTriggerVariant,
final int minBaseQual,
final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) {
final ReduceReads.DownsampleStrategy downsampleStrategy) {
this.sampleName = sampleName;
this.contextSize = contextSize;
this.downsampleCoverage = downsampleCoverage;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -53,7 +53,7 @@ public class SlidingWindow {
protected int MIN_BASE_QUAL_TO_COUNT; // qual has to be greater than or equal to this value
protected int MIN_MAPPING_QUALITY;
protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy;
protected ReduceReads.DownsampleStrategy downsampleStrategy;
private boolean hasIndelQualities;
/**
@ -82,7 +82,7 @@ public class SlidingWindow {
}
public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReadsWalker.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) {
public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) {
this.stopLocation = -1;
this.contextSize = contextSize;
this.downsampleCoverage = downsampleCoverage;

22
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -33,20 +33,21 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
@ -56,6 +57,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.FileNotFoundException;
import java.io.PrintStream;
@ -90,7 +92,7 @@ import java.util.*;
@PartitionBy(PartitionType.LOCUS)
@ActiveRegionExtension(extension=65, maxRegion=275)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatibleWalker {
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
/**
* A raw, unfiltered, highly specific callset in VCF format.
@ -361,7 +363,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
//---------------------------------------------------------------------------------------------------------------
@Override
public Integer map( final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
final ArrayList<VariantContext> activeAllelesToGenotype = new ArrayList<VariantContext>();
@ -476,7 +478,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
//
//---------------------------------------------------------------------------------------------------------------
private void finalizeActiveRegion( final ActiveRegion activeRegion ) {
private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getExtendedLoc() + " with " + activeRegion.size() + " reads:"); }
final ArrayList<GATKSAMRecord> finalizedReadList = new ArrayList<GATKSAMRecord>();
final FragmentCollection<GATKSAMRecord> fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) );
@ -503,7 +505,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
}
}
private List<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
private List<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
final ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
for( final GATKSAMRecord rec : activeRegion.getReads() ) {
if( rec.getReadLength() < 24 || rec.getMappingQuality() <= 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
@ -514,7 +516,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
return readsToRemove;
}
private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) {
private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
final int padLeft = Math.max(activeRegion.getReferenceLoc().getStart()-REFERENCE_PADDING, 1);
final int padRight = Math.min(activeRegion.getReferenceLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReferenceLoc().getContig()).getSequenceLength());
return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReferenceLoc().getContig(), padLeft, padRight);

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java → public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -46,7 +46,7 @@ import java.util.Iterator;
* @author mhanna
* @version 0.1
*/
public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
public class AlignmentValidation extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.
*/

2
public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java → public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java
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@ -48,7 +48,7 @@ import java.util.TreeMap;
* @author mhanna
* @version 0.1
*/
public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
public class CountBestAlignments extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.
*/

38
public/java/src/org/broadinstitute/sting/gatk/Categorize.java 100644
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@ -0,0 +1,38 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk;
import java.lang.annotation.*;
/**
* Allows the walker to be tagged, they can have an unlimited number of categories.
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface Categorize {
public Category[] value() default {Category.UNCATEGORIZED};
}

68
public/java/src/org/broadinstitute/sting/gatk/Category.java 100644
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@ -0,0 +1,68 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk;
public enum Category {
BAM_PROCESSING("Walker", "BAM Processing and Analysis Tools"),
COMPANION("Walker", "Companion Utilities"),
CANCER_SPECIFIC("Walker", "Cancer-specific Variant Discovery Tools"),
QUALITY_CONTROL("Walker", "Quality Control and Simple Analysis Tools"),
VALIDATION("Walker", "Validation Utilities"),
VARIANT_DETECTION("ex", "Variant Detection"),
VARIANT_DISCOVERY("Walker", "Variant Discovery Tools"),
VARIANT_EVALUATION("Walker", "Variant Evaluation and Manipulation Tools"),
EXPERIMENTAL("Walker", "Miscellaneous Experimental (and Potentially Unstable) Tools"),
UNCATEGORIZED("all", "No category");
private final String description;
/**
* Accepted strings are from the GATKDocWorkUnit.group
*/
private final String type;
private Category(String type, String description) {
this.description = description;
this.type = type;
}
public String type() {
return type;
}
public String getDescription() {
return description;
}
}

1
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.SampleUtils;

28
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -6,10 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfile;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -28,7 +30,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
*/
protected static Logger logger = Logger.getLogger(TraversalEngine.class);
private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
private final LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue = new LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion>();
private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
@Override
@ -109,18 +111,18 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// add these blocks of work to the work queue
// band-pass filter the list of isActive probabilities and turn into active regions
final ActivityProfile bandPassFiltered = profile.bandPassFilter();
final List<ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize );
final List<org.broadinstitute.sting.utils.activeregion.ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize );
// add active regions to queue of regions to process
// first check if can merge active regions over shard boundaries
if( !activeRegions.isEmpty() ) {
if( !workQueue.isEmpty() ) {
final ActiveRegion last = workQueue.getLast();
final ActiveRegion first = activeRegions.get(0);
final org.broadinstitute.sting.utils.activeregion.ActiveRegion last = workQueue.getLast();
final org.broadinstitute.sting.utils.activeregion.ActiveRegion first = activeRegions.get(0);
if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= maxRegionSize ) {
workQueue.removeLast();
activeRegions.remove(first);
workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) );
workQueue.add( new org.broadinstitute.sting.utils.activeregion.ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) );
}
}
workQueue.addAll( activeRegions );
@ -183,7 +185,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
*/
private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) {
// Just want to output the active regions to a file, not actually process them
for( final ActiveRegion activeRegion : workQueue ) {
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) {
if( activeRegion.isActive ) {
walker.activeRegionOutStream.println( activeRegion.getLocation() );
}
@ -196,7 +198,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
while( workQueue.peek() != null ) {
final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc();
if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) {
final ActiveRegion activeRegion = workQueue.remove();
final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion = workQueue.remove();
sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker );
} else {
break;
@ -206,15 +208,15 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
return sum;
}
private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
for( final GATKSAMRecord read : reads ) {
final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read );
if( activeRegion.getLocation().overlapsP( readLoc ) ) {
// The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region)
long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc );
ActiveRegion bestRegion = activeRegion;
for( final ActiveRegion otherRegionToTest : workQueue ) {
org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion;
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) {
maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc );
bestRegion = otherRegionToTest;
@ -227,7 +229,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
if( !bestRegion.equals(activeRegion) ) {
activeRegion.add( read );
}
for( final ActiveRegion otherRegionToTest : workQueue ) {
for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
otherRegionToTest.add( read );
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
View File

@ -12,7 +12,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
@ -76,7 +75,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
public abstract double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
// Map over the ActiveRegion
public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
public abstract MapType map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
View File

@ -149,7 +149,7 @@ import java.util.regex.Pattern;
* @since 2010
*/
@Requires({DataSource.READS})
public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
/**
* If provided, ClipReads will write summary statistics about the clipping operations applied
* to the reads to this file.

2
public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java
View File

@ -49,7 +49,7 @@ import java.util.Set;
*/
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
@Requires({DataSource.READS, DataSource.REFERENCE})
public class FindReadsWithNamesWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
public class FindReadsWithNames extends ReadWalker<SAMRecord, SAMFileWriter> {
/** an optional argument to dump the reads out to a BAM file */
@Output(doc="Write output to this BAM filename instead of STDOUT")
SAMFileWriter out;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
View File

@ -42,12 +42,12 @@ import java.text.NumberFormat;
* @author aaron
*/
@Requires({DataSource.READS})
public class FlagStatWalker extends ReadWalker<Integer, Integer> {
public class FlagStat extends ReadWalker<Integer, Integer> {
@Output
PrintStream out;
// what comes out of the flagstat
static class FlagStat {
static class FlagStatus {
long readCount = 0L;
long QC_failure = 0L;
long duplicates = 0L;
@ -117,7 +117,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
}
private FlagStat myStat = new FlagStat();
private FlagStatus myStat = new FlagStatus();
public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
myStat.readCount++;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
View File

@ -60,7 +60,7 @@ import java.util.List;
* Associated command:
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
*/
public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
@Output
PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
View File

@ -39,7 +39,7 @@ import java.io.PrintStream;
* Prints out all of the RODs in the input data set. Data is rendered using the toString() method
* of the given ROD.
*/
public class PrintRODsWalker extends RodWalker<Integer, Integer> {
public class PrintRODs extends RodWalker<Integer, Integer> {
@Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true)
public RodBinding<Feature> input;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
View File

@ -90,7 +90,7 @@ import java.util.TreeSet;
*/
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
@Requires({DataSource.READS, DataSource.REFERENCE})
public class PrintReadsWalker extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
@Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
SAMFileWriter out;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
View File

@ -47,14 +47,14 @@ import java.util.Map;
*/
@WalkerName("SplitSamFile")
@Requires({DataSource.READS})
public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
@Argument(fullName="outputRoot", doc="output BAM file", required=false)
public String outputRoot = null;
@Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
public Integer BAMcompression = 5;
private static Logger logger = Logger.getLogger(SplitSamFileWalker.class);
private static Logger logger = Logger.getLogger(SplitSamFile.class);
private static String VERSION = "0.0.1";
public void initialize() {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -51,7 +51,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
char[] BASES = {'A','C','G','T'};
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
@ -14,7 +14,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
/**
@ -22,7 +24,7 @@ import java.util.*;
*/
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
Double ratio = annotateSNP(stratifiedContext, vc, g);
if (ratio == null)
return;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
View File

@ -34,7 +34,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -52,7 +52,7 @@ import java.util.Map;
*/
public class BaseCounts extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
View File

@ -29,18 +29,17 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -62,14 +61,14 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
private Set<String> founderIds = new HashSet<String>();
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.hasGenotypes() )
return null;
return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap<String, Object>(), true,founderIds);
}
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ){
public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ){
//If families were given, get the founders ids
founderIds = ((Walker)walker).getSampleDB().getFounderIds();
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
@ -38,7 +38,7 @@ import java.util.Map;
*/
public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -3,10 +3,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -14,7 +16,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
/**
@ -42,7 +46,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) {
if ( g == null || !g.isCalled() )
return;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
@ -55,7 +55,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
private static final String FS = "FS";
private static final double MIN_PVALUE = 1E-320;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isVariant() )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.BaseUtils;
@ -22,7 +22,7 @@ import java.util.Map;
*/
public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
double content = computeGCContent(ref);
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", content));

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -28,7 +28,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
@ -60,7 +60,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
private final static char REGEXP_WILDCARD = '.';
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
View File

@ -4,7 +4,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
import org.broadinstitute.sting.utils.QualityUtils;
@ -29,7 +29,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
private static final int MIN_GENOTYPE_QUALITY = 10;
private static final int MIN_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
final GenotypesContext genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
View File

@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -23,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation {
private boolean ANNOTATE_INDELS = true;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isBiallelic() )
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
View File

@ -3,9 +3,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
@ -33,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
private static final int MIN_SAMPLES = 10;
private Set<String> founderIds;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
//If available, get the founder IDs and cache them. the IC will only be computed on founders then.
if(founderIds == null)
founderIds = ((Walker)walker).getSampleDB().getFounderIds();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.IndelUtils;
@ -18,7 +18,7 @@ import java.util.*;
*/
public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
int run;
if (vc.isMixed()) {

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
View File

@ -3,12 +3,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -22,7 +21,7 @@ import java.util.Map;
*/
public class LowMQ extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.samples.SampleDB;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
@ -32,7 +32,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
private String fatherId;
private String childId;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( mendelianViolation == null ) {
if (checkAndSetSamples(((Walker) walker).getSampleDB())) {
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
@ -24,7 +24,7 @@ import java.util.Map;
*/
public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
@ -47,7 +47,7 @@ import java.util.List;
*/
public class MappingQualityZeroBySample extends GenotypeAnnotation {
public void annotate(RefMetaDataTracker tracker,
AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context,
AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context,
VariantContext vc, Genotype g, GenotypeBuilder gb) {
if ( g == null || !g.isCalled() )
return;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -22,7 +22,7 @@ import java.util.Map;
*/
public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -20,7 +20,7 @@ import java.util.Map;
* The number of N bases, counting only SOLiD data
*/
public class NBaseCount extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -28,7 +28,7 @@ import java.util.Map;
*/
public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.hasLog10PError() || stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
@ -29,7 +29,7 @@ import java.util.Map;
*/
public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
View File

@ -4,9 +4,8 @@ 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.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.utils.MannWhitneyU;
import org.broadinstitute.sting.utils.QualityUtils;
@ -32,7 +31,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
static final double INDEL_LIKELIHOOD_THRESH = 0.1;
static final boolean DEBUG = false;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if (stratifiedContexts.size() == 0)
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -46,7 +46,7 @@ import java.util.Map;
*/
public class SampleList extends InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( vc.isMonomorphicInSamples() || !vc.hasGenotypes() )
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.Utils;
@ -203,7 +203,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
}
}
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
// Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
// without providing a SnpEff rod via --snpEffFile):
validateRodBinding(walker.getSnpEffRodBinding());
@ -225,7 +225,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue()));
}
public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
// Get only SnpEff records that start at this locus, not merely span it:

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -22,7 +22,7 @@ import java.util.Map;
*/
public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
View File

@ -27,10 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -48,7 +47,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
private static final String STR_PRESENT = "STR";
private static final String REPEAT_UNIT_KEY = "RU";
private static final String REPEATS_PER_ALLELE_KEY = "RPA";
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isIndel())
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Hidden;
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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -28,7 +28,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
private String n454 ="Num454";
private String nSolid = "NumSOLiD";
private String nOther = "NumOther";
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
@ -28,7 +28,7 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
private Set<Sample> trios = null;
private final static int MIN_NUM_VALID_TRIOS = 5; // don't calculate this population-level statistic if there are less than X trios with full genotype likelihood information
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( trios == null ) {
if ( walker instanceof VariantAnnotator ) {
trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -38,8 +38,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.util.*;
@ -79,7 +79,7 @@ import java.util.*;
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@Reference(window=@Window(start=-50,stop=50))
@By(DataSource.REFERENCE)
public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatibleWalker {
public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -46,7 +46,7 @@ public class VariantAnnotatorEngine {
private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
private final HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
private final AnnotatorCompatibleWalker walker;
private final AnnotatorCompatible walker;
private final GenomeAnalysisEngine toolkit;
private boolean requireStrictAlleleMatch = false;
@ -75,7 +75,7 @@ public class VariantAnnotatorEngine {
}
// use this constructor if you want all possible annotations
public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) {
this.walker = walker;
this.toolkit = toolkit;
requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
@ -85,7 +85,7 @@ public class VariantAnnotatorEngine {
}
// use this constructor if you want to select specific annotations (and/or interfaces)
public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) {
this.walker = walker;
this.toolkit = toolkit;
initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
View File

@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
public interface AnnotatorCompatibleWalker {
public interface AnnotatorCompatible {
// getter methods for various used bindings
public abstract RodBinding<VariantContext> getSnpEffRodBinding();

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
View File

@ -9,12 +9,11 @@ import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample
public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker,
ReferenceContext ref, AlignmentContext stratifiedContext,
VariantContext vc, Genotype g, GenotypeBuilder gb );

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
View File

@ -11,7 +11,7 @@ import java.util.Map;
public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts split by sample
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker,
ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
// return the descriptions used for the VCF INFO meta field

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
View File

@ -37,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation {
public abstract List<String> getKeyNames();
// initialization method (optional for subclasses, and therefore non-abstract)
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
View File

@ -31,13 +31,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.util.*;
@ -72,7 +72,7 @@ import static java.lang.Math.log10;
<p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
*/
public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

9
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
View File

@ -37,10 +37,13 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.File;
import java.io.PrintStream;
@ -72,7 +75,7 @@ import java.util.*;
*
*/
public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
View File

@ -38,12 +38,12 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream;
import java.util.Arrays;
@ -54,7 +54,7 @@ import java.util.Set;
* in input variant file. Will additional hold back a fraction of the sites for evaluation, marking the
* genotypes at that sites as missing, and writing the truth of these sites to a second VCF file
*/
public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer> {
public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@ -104,7 +104,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer>
GenomeLoc loc = context.getLocation();
VariantContext vc = tracker.getFirstValue(variants, loc);
if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) {
if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) {
// do we want to hold back this site?
boolean makeMissing = dropSite(vc);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java → public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
View File

@ -47,7 +47,7 @@ import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.lang.reflect.Constructor;
import java.util.*;
import java.util.ArrayList;
/**
* First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide).
@ -106,7 +106,7 @@ import java.util.*;
@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality
@PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
public class BQSR extends LocusWalker<Long, Long> implements TreeReducible<Long> {
@ArgumentCollection
private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
View File

@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
* @return the covariate keysets for this read
*/
protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE);
return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE);
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
View File

@ -120,7 +120,7 @@ import java.io.PrintStream;
* @since May 7, 2010
*/
@By(DataSource.REFERENCE)
public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableBaseState, CallableLociWalker.Integrator> {
public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
@Output
PrintStream out;

34
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
View File

@ -41,7 +41,7 @@ import java.util.List;
/**
* Test routine for new VariantContext object
*/
public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker.CallableBaseState>, long[][]> {
public class CompareCallableLoci extends RodWalker<List<CallableLoci.CallableBaseState>, long[][]> {
@Output
protected PrintStream out;
@ -54,8 +54,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
@Argument(shortName="printState", doc="If provided, prints sites satisfying this state pair", required=false)
protected String printState = null;
CallableLociWalker.CalledState printState1 = CallableLociWalker.CalledState.REF_N;
CallableLociWalker.CalledState printState2 = CallableLociWalker.CalledState.REF_N;
CallableLoci.CalledState printState1 = CallableLoci.CalledState.REF_N;
CallableLoci.CalledState printState2 = CallableLoci.CalledState.REF_N;
// --------------------------------------------------------------------------------------------------------------
//
@ -66,8 +66,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
public void initialize() {
if ( printState != null ) {
String[] states = printState.split(",");
printState1 = CallableLociWalker.CalledState.valueOf(states[0]);
printState2 = CallableLociWalker.CalledState.valueOf(states[1]);
printState1 = CallableLoci.CalledState.valueOf(states[0]);
printState2 = CallableLoci.CalledState.valueOf(states[1]);
}
}
@ -77,10 +77,10 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
// map
//
// --------------------------------------------------------------------------------------------------------------
public List<CallableLociWalker.CallableBaseState> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public List<CallableLoci.CallableBaseState> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker != null ) {
CallableLociWalker.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1);
CallableLociWalker.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2);
CallableLoci.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1);
CallableLoci.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2);
if ( printState != null && comp1.getState() == printState1 && comp2.getState() == printState2 ) {
out.printf("%s %s %s %s%n", comp1.getLocation(), comp1.getState(), comp2.getLocation(), comp2.getState());
@ -92,7 +92,7 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
}
}
private CallableLociWalker.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding<BEDFeature> rodBinding) {
private CallableLoci.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding<BEDFeature> rodBinding) {
//System.out.printf("tracker %s%n", tracker);
List<BEDFeature> bindings = tracker.getValues(rodBinding);
if ( bindings.size() != 1 ) {
@ -101,8 +101,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
BEDFeature bed = bindings.get(0);
GenomeLoc loc = getToolkit().getGenomeLocParser().createGenomeLoc(bed.getChr(), bed.getStart(), bed.getEnd());
CallableLociWalker.CalledState state = CallableLociWalker.CalledState.valueOf(bed.getName());
return new CallableLociWalker.CallableBaseState(getToolkit().getGenomeLocParser(),loc, state);
CallableLoci.CalledState state = CallableLoci.CalledState.valueOf(bed.getName());
return new CallableLoci.CallableBaseState(getToolkit().getGenomeLocParser(),loc, state);
}
// --------------------------------------------------------------------------------------------------------------
@ -111,14 +111,14 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
//
// --------------------------------------------------------------------------------------------------------------
public long[][] reduceInit() {
int n = CallableLociWalker.CalledState.values().length;
int n = CallableLoci.CalledState.values().length;
return new long[n][n];
}
public long[][] reduce(List<CallableLociWalker.CallableBaseState> comps, long[][] sum) {
public long[][] reduce(List<CallableLoci.CallableBaseState> comps, long[][] sum) {
if ( comps != null ) {
CallableLociWalker.CallableBaseState comp1 = comps.get(0);
CallableLociWalker.CallableBaseState comp2 = comps.get(1);
CallableLoci.CallableBaseState comp1 = comps.get(0);
CallableLoci.CallableBaseState comp2 = comps.get(1);
sum[comp1.getState().ordinal()][comp2.getState().ordinal()]++;
}
@ -127,8 +127,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
}
public void onTraversalDone(long[][] result) {
for ( CallableLociWalker.CalledState state1 : CallableLociWalker.CalledState.values() ) {
for ( CallableLociWalker.CalledState state2 : CallableLociWalker.CalledState.values() ) {
for ( CallableLoci.CalledState state1 : CallableLoci.CalledState.values() ) {
for ( CallableLoci.CalledState state2 : CallableLoci.CalledState.values() ) {
out.printf("%s %s %s %s %d%n", compTrack1.getName(), compTrack2.getName(), state1, state2, result[state1.ordinal()][state2.ordinal()]);
}
}

8
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
View File

@ -34,9 +34,6 @@ 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.refdata.SeekableRODIterator;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
@ -45,6 +42,9 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -117,7 +117,7 @@ import java.util.*;
@By(DataSource.REFERENCE)
@PartitionBy(PartitionType.NONE)
@Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
@Output
@Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
Map<DoCOutputType,PrintStream> out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
View File

@ -63,7 +63,7 @@ import java.util.List;
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE})
@By(DataSource.REFERENCE)
public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
public class GCContentByInterval extends LocusWalker<Long, Long> {
@Output
protected PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
View File

@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import java.io.PrintStream;
@ -56,7 +55,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
}
@Override
public GenomeLoc map(final ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
if (activeRegion.isActive)
return activeRegion.getLocation();
else

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
View File

@ -131,7 +131,7 @@ import java.util.List;
* @author Mark DePristo
* @since 7/4/11
*/
public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
public class DiffObjects extends RodWalker<Integer, Integer> {
/**
* Writes out a file of the DiffEngine format:
*

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
View File

@ -73,7 +73,7 @@ import java.util.List;
@WalkerName("FastaAlternateReferenceMaker")
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
public class FastaAlternateReference extends FastaReference {
/**
* Variants from these input files are used by this tool to construct an alternate reference.

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
View File

@ -67,7 +67,7 @@ import java.io.PrintStream;
*
*/
@WalkerName("FastaReferenceMaker")
public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
@Output PrintStream out;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
View File

@ -37,10 +37,10 @@ import java.io.PrintStream;
/**
* Calculates basic statistics about the reference sequence itself
*/
public class FastaStatsWalker extends RefWalker<Byte, FastaStatsWalker.FastaStats> {
public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
@Output PrintStream out;
protected class FastaStats {
protected class FastaStatistics {
long nBases = 0, nRegBases = 0;
}
@ -50,19 +50,19 @@ public class FastaStatsWalker extends RefWalker<Byte, FastaStatsWalker.FastaStat
}
@Override
public FastaStats reduceInit() {
return new FastaStats();
public FastaStatistics reduceInit() {
return new FastaStatistics();
}
@Override
public FastaStats reduce(Byte base, FastaStats stats) {
public FastaStatistics reduce(Byte base, FastaStatistics stats) {
stats.nBases++;
if (BaseUtils.isRegularBase(base)) stats.nRegBases++;
return stats;
}
@Override
public void onTraversalDone(FastaStats sum) {
public void onTraversalDone(FastaStatistics sum) {
out.printf("Total bases %d%n", sum.nBases);
out.printf("Regular bases %d%n", sum.nRegBases);
}

8
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
View File

@ -31,13 +31,15 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
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.*;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.util.*;
@ -74,7 +76,7 @@ import java.util.*;
*
*/
@Reference(window=@Window(start=-50,stop=50))
public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
public class VariantFiltration extends RodWalker<Integer, Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -35,16 +35,16 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream;
import java.util.*;
@ -121,7 +121,7 @@ import java.util.*;
// TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources:
// TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} )
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker {
public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatible {
@ArgumentCollection
private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();

5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.*;
import org.apache.commons.jexl2.Expression;
import org.apache.commons.jexl2.JexlContext;
import org.apache.commons.jexl2.JexlEngine;
@ -53,7 +52,6 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.collections.CircularArray;
import org.broadinstitute.sting.utils.collections.PrimitivePair;
import org.broadinstitute.sting.utils.exceptions.StingException;
@ -64,6 +62,7 @@ import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.*;
import java.util.*;
@ -127,7 +126,7 @@ import java.util.*;
*/
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
// @Output
// PrintStream out;
@Output(doc="File to write variants (indels) in VCF format",required=true)

4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
View File

@ -113,7 +113,7 @@ class PhasingUtils {
Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
if (phaseQual.PQ != null)
mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
mergedGtAttribs.put(ReadBackedPhasing.PQ_KEY, phaseQual.PQ);
Genotype mergedGt = new GenotypeBuilder(gt1.getSampleName(), mergedAllelesForSample).log10PError(mergedGQ).attributes(mergedGtAttribs).phased(phaseQual.isPhased).make();
mergedGenotypes.add(mergedGt);
@ -373,7 +373,7 @@ class PhasingUtils {
public PhaseAndQuality(Genotype gt) {
this.isPhased = gt.isPhased();
if (this.isPhased) {
this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1);
this.PQ = gt.getAttributeAsDouble(ReadBackedPhasing.PQ_KEY, -1);
if ( this.PQ == -1 ) this.PQ = null;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
View File

@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
// Filter out all reads with zero mapping quality
@ReadFilters({MappingQualityZeroFilter.class})
public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false;
/**
* The VCF file we are phasing variants from.
@ -255,7 +255,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
for (VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {
if (ReadBackedPhasing.processVariantInPhasing(vc)) {
VariantAndReads vr = new VariantAndReads(vc, context);
unphasedSiteQueue.add(vr);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
View File

@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
*
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountBasesWalker extends ReadWalker<Integer, Long> {
public class CountBases extends ReadWalker<Integer, Long> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
return read.getReadLength();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
View File

@ -37,7 +37,7 @@ import java.io.PrintStream;
* </pre>
*
*/
public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@Output(doc="Write count to this file instead of STDOUT")
PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
View File

@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* --read-filter command line argument). Simplest example of a read-backed analysis.
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountMalesWalker extends ReadWalker<Integer, Integer> {
public class CountMales extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
Sample sample = getSampleDB().getSample(read);
return sample.getGender() == Gender.MALE ? 1 : 0;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
View File

@ -70,7 +70,7 @@ import java.util.*;
* </pre>
*
*/
public class CountRODsWalker extends RodWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
@Output
public PrintStream out;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
View File

@ -63,7 +63,7 @@ import java.util.List;
* </pre>
*
*/
public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
public class CountRODsByRef extends RefWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> {
/**
* One or more input rod files
@ -77,14 +77,14 @@ public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<
@Argument(fullName = "showSkipped", shortName = "s", doc="If true, this tool will print out the skipped locations", required = false)
public boolean showSkipped = false;
CountRODsWalker crw = new CountRODsWalker();
CountRODs crw = new CountRODs();
public void initialize() {
crw.verbose = verbose;
crw.showSkipped = showSkipped;
}
public CountRODsWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public CountRODs.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return crw.map(tracker, ref, context);
}
@ -92,7 +92,7 @@ public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<
return crw.reduceInit();
}
public Pair<ExpandingArrayList<Long>, Long> reduce(CountRODsWalker.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
public Pair<ExpandingArrayList<Long>, Long> reduce(CountRODs.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
return crw.reduce(point, sum);
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
View File

@ -42,7 +42,7 @@ import java.util.Map;
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadEventsWalker extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
@Output (doc = "GATKReport table output")
PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
View File

@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
*
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadsWalker extends ReadWalker<Integer, Integer> {
public class CountReads extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
return 1;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
View File

@ -37,7 +37,7 @@ import java.util.List;
* </pre>
*/
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountTerminusEventWalker extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
List<CigarElement> cigarElements = read.getCigar().getCigarElements();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java
View File

@ -56,7 +56,7 @@ import java.util.*;
* --read-filter command line argument). Simplest example of a read-backed analysis.
*/
@Requires({DataSource.READS})
public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
public class CycleQuality extends ReadWalker<Integer,Integer> {
@Output
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
View File

@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
/**
* a walker that simply throws errors. Allows us to test that the engine is behaving as expected with error handling
*/
public class ErrorThrowingWalker extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
public class ErrorThrowing extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
@Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true)
public String exceptionToThrow;

11
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
View File

@ -26,24 +26,15 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.SAMSequenceRecord;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
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.RefWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.PrintStream;
import java.util.Collections;
import java.util.List;
/**
* Prints out counts of the number of reference ordered data objects encountered.
@ -67,7 +58,7 @@ import java.util.List;
* </pre>
*
*/
public class QCRefWalker extends RefWalker<Integer, Integer> {
public class QCRef extends RefWalker<Integer, Integer> {
@Output
public PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
View File

@ -52,7 +52,7 @@ import java.util.Arrays;
* of the clipping to the output stream.
*/
@Requires({DataSource.READS})
public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
@Output
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java
View File

@ -44,7 +44,7 @@ import java.util.List;
* the same read is not passed to the walker multiple consecutive times.
* @author aaron
*/
public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
public class ReadValidation extends ReadWalker<SAMRecord, SAMRecord> {
// our MD5 sum
private MessageDigest m;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
View File

@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
@ -51,7 +50,7 @@ import java.util.List;
* a walker for validating (in the style of validating pile-up) the ROD system.
*/
@Reference(window=@Window(start=-40,stop=40))
public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
public class RodSystemValidation extends RodWalker<Integer,Integer> {
// the divider to use in some of the text output
private static final String DIVIDER = ",";

9
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
View File

@ -32,9 +32,12 @@ import org.broadinstitute.sting.commandline.RodBinding;
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.utils.codecs.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -48,7 +51,7 @@ import java.util.Arrays;
* should be specified using the command-line argument '-B pileup,SAMPileup,<your sam pileup file>'.
*/
@Requires(value={DataSource.READS,DataSource.REFERENCE})
public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
@Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true)
RodBinding<SAMPileupFeature> pileup;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
View File

@ -38,10 +38,10 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.util.Map;
import java.util.Set;
@ -195,7 +195,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
@Reference(window=@Window(start=-200,stop=200))
public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> implements TreeReducible<GenotypeAndValidateWalker.CountedData> {
public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedData, GenotypeAndValidate.CountedData> implements TreeReducible<GenotypeAndValidate.CountedData> {
/**
* The optional output file that will have all the variants used in the Genotype and Validation essay.

8
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
View File

@ -30,10 +30,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.File;
import java.util.*;
@ -94,7 +96,7 @@ import java.util.*;
* </pre>
*
*/
public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
public enum AF_COMPUTATION_MODE {
KEEP_AF_SPECTRUM,

3
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import com.google.java.contract.Requires;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.util.IntervalTree;
import net.sf.samtools.SAMSequenceRecord;
@ -88,7 +87,7 @@ import java.util.*;
*/
@Reference(window=@Window(start=-50, stop=50))
@PartitionBy(PartitionType.NONE)
public class VariantEvalWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
public class VariantEval extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
public static final String IS_SINGLETON_KEY = "ISSINGLETON";
@Output

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.MendelianViolation;
@ -104,7 +104,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
MendelianViolation mv;
Map<String,Set<Sample>> families;
public void initialize(VariantEvalWalker walker) {
public void initialize(VariantEval walker) {
super.initialize(walker);
mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false);
families = walker.getSampleDB().getFamilies();

10
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
View File

@ -3,23 +3,23 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
private VariantEvalWalker walker;
private VariantEval walker;
private final String simpleName;
protected VariantEvaluator() {
this.simpleName = getClass().getSimpleName();
}
public void initialize(VariantEvalWalker walker) {
public void initialize(VariantEval walker) {
this.walker = walker;
}
public VariantEvalWalker getWalker() {
public VariantEval getWalker() {
return walker;
}
@ -57,7 +57,7 @@ public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
* @return true if eval was originally a singleton site
*/
protected static boolean variantWasSingleton(final VariantContext eval) {
return eval.getAttributeAsBoolean(VariantEvalWalker.IS_SINGLETON_KEY, false);
return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false);
}
public final String getSimpleName() {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
View File

@ -29,7 +29,7 @@ import org.apache.log4j.Logger;
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.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -150,7 +150,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
}
public void initialize(VariantEvalWalker walker) {
public void initialize(VariantEval walker) {
super.initialize(walker);
nSamples = walker.getSampleNamesForEvaluation().size();

8
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -13,7 +13,7 @@ import java.util.List;
import java.util.Set;
public abstract class VariantStratifier implements Comparable<VariantStratifier>, Stratifier {
private VariantEvalWalker variantEvalWalker;
private VariantEval variantEvalWalker;
final private String name;
final protected ArrayList<Object> states = new ArrayList<Object>();
@ -40,7 +40,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
/**
* @return a reference to the parent VariantEvalWalker running this stratification
*/
public final VariantEvalWalker getVariantEvalWalker() {
public final VariantEval getVariantEvalWalker() {
return variantEvalWalker;
}
@ -48,7 +48,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
* Should only be called by VariantEvalWalker itself
* @param variantEvalWalker
*/
public final void setVariantEvalWalker(VariantEvalWalker variantEvalWalker) {
public final void setVariantEvalWalker(VariantEval variantEvalWalker) {
this.variantEvalWalker = variantEvalWalker;
}

14
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
View File

@ -3,27 +3,27 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util;
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.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
import java.util.ArrayList;
import java.util.Set;
import java.util.TreeSet;
public final class EvaluationContext {
// NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function
final VariantEvalWalker walker;
final VariantEval walker;
private final ArrayList<VariantEvaluator> evaluationInstances;
private final Set<Class<? extends VariantEvaluator>> evaluationClasses;
public EvaluationContext(final VariantEvalWalker walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
public EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
this(walker, evaluationClasses, true);
}
private EvaluationContext(final VariantEvalWalker walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
private EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
this.walker = walker;
this.evaluationClasses = evaluationClasses;
this.evaluationInstances = new ArrayList<VariantEvaluator>(evaluationClasses.size());

10
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
View File

@ -28,7 +28,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
@ -45,10 +45,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.*;
public class VariantEvalUtils {
private final VariantEvalWalker variantEvalWalker;
private final VariantEval variantEvalWalker;
Logger logger;
public VariantEvalUtils(VariantEvalWalker variantEvalWalker) {
public VariantEvalUtils(VariantEval variantEvalWalker) {
this.variantEvalWalker = variantEvalWalker;
this.logger = variantEvalWalker.getLogger();
}
@ -216,7 +216,7 @@ public class VariantEvalUtils {
VariantContextBuilder builder = new VariantContextBuilder(vcsub);
if ( isSingleton )
builder.attribute(VariantEvalWalker.IS_SINGLETON_KEY, true);
builder.attribute(VariantEval.IS_SINGLETON_KEY, true);
if ( ! hasChrCountAnnotations )
VariantContextUtils.calculateChromosomeCounts(builder, true);
@ -270,7 +270,7 @@ public class VariantEvalUtils {
}
if ((byFilter || !vcsub.isFiltered())) {
addMapping(mapping, VariantEvalWalker.getAllSampleName(), vcsub);
addMapping(mapping, VariantEval.getAllSampleName(), vcsub);
}
// Now, if stratifying, split the subsetted vc per sample and add each as a new context

15
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
View File

@ -1,5 +1,5 @@
/*
* Copyright (c) 2011, The Broad Institute
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -25,11 +25,17 @@
package org.broadinstitute.sting.utils.help;
public class GATKDocUtils {
/** The URL root for RELEASED GATKDOC units */
/**
* The URL root for RELEASED GATKDOC units
*/
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
/** The URL root for STABLE GATKDOC units */
/**
* The URL root for STABLE GATKDOC units
*/
public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
/** The URL root for UNSTABLE GATKDOC units */
/**
* The URL root for UNSTABLE GATKDOC units
*/
public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
/**
@ -49,6 +55,7 @@ public class GATKDocUtils {
/**
* Returns a full URL http://etc/ linking to the documentation for class (assuming it
* exists). Currently points to the RELEASE doc path only.
*
* @param c
* @return
*/

48
public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java
View File

@ -1,5 +1,5 @@
/*
* Copyright (c) 2011, The Broad Institute
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -25,41 +25,63 @@
package org.broadinstitute.sting.utils.help;
import com.sun.javadoc.ClassDoc;
import org.broadinstitute.sting.gatk.Category;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Simple collection of all relevant information about something the GATKDoclet can document
*
* <p/>
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/24/11
* Time: 7:59 PM
*/
class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
/** The class that's being documented */
/**
* The class that's being documented
*/
final Class clazz;
/** The name of the thing we are documenting */
/**
* The name of the thing we are documenting
*/
final String name;
/** the filename where we will be writing the docs for this class */
/**
* the filename where we will be writing the docs for this class
*/
final String filename;
/** The name of the documentation group (e.g., walkers, read filters) class belongs to */
/**
* The name of the documentation group (e.g., walkers, read filters) class belongs to
*/
final String group;
/** The documentation handler for this class */
/**
* The categories that this class belongs to
*/
final List<Category> categories;
/**
* The documentation handler for this class
*/
final DocumentedGATKFeatureHandler handler;
/** The javadoc documentation for clazz */
/**
* The javadoc documentation for clazz
*/
final ClassDoc classDoc;
/** The annotation that lead to this Class being in GATKDoc */
/**
* The annotation that lead to this Class being in GATKDoc
*/
final DocumentedGATKFeatureObject annotation;
/** When was this walker built, and what's the absolute version number */
/**
* When was this walker built, and what's the absolute version number
*/
final String buildTimestamp, absoluteVersion;
// set by the handler
String summary;
Map<String, Object> forTemplate;
public GATKDocWorkUnit(String name, String filename, String group,
public GATKDocWorkUnit(String name, String filename, String group, List<Category> categories,
DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler,
ClassDoc classDoc, Class clazz,
String buildTimestamp, String absoluteVersion) {
@ -67,6 +89,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
this.name = name;
this.filename = filename;
this.group = group;
this.categories = categories;
this.handler = handler;
this.classDoc = classDoc;
this.clazz = clazz;
@ -76,6 +99,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
/**
* Called by the GATKDoclet to set handler provided context for this work unit
*
* @param summary
* @param forTemplate
*/
@ -86,6 +110,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
/**
* Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit
*
* @return
*/
public Map<String, String> indexDataMap() {
@ -99,6 +124,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
/**
* Sort in order of the name of this WorkUnit
*
* @param other
* @return
*/

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