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Adding extraDocs tag per Mauricio's request

This commit is contained in:
Eric Banks 2012-07-25 18:23:18 -04:00
parent 05fa377a8e
commit 0a98a6aa8d
36 changed files with 71 additions and 35 deletions
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1
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -29,6 +29,7 @@ import com.google.java.contract.Ensures;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -100,7 +101,7 @@ import java.util.*;
* @since 8/22/11
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
@ActiveRegionExtension(extension=65, maxRegion=275)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@ -149,7 +150,7 @@ import java.util.regex.Pattern;
* @author Mark DePristo
* @since 2010
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
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@ -29,6 +29,7 @@ import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@ -89,7 +90,7 @@ import java.util.TreeSet;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
@Requires({DataSource.READS, DataSource.REFERENCE})
public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -21,7 +22,7 @@ import java.util.Map;
/**
* The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -76,7 +77,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Requires(value={})
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@Reference(window=@Window(start=-50,stop=50))

3
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -73,7 +74,7 @@ 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>
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
@ArgumentCollection

3
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -76,7 +77,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

3
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
@ -98,7 +99,7 @@ import java.util.ArrayList;
* </pre>
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
@By(DataSource.READS)
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file

3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -120,7 +121,7 @@ import java.io.PrintStream;
* @author Mark DePristo
* @since May 7, 2010
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@By(DataSource.REFERENCE)
public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
@Output

3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
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@ -29,6 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -115,7 +116,7 @@ import java.util.*;
// todo -- alter logarithmic scaling to spread out bins more
// todo -- allow for user to set linear binning (default is logarithmic)
// todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@By(DataSource.REFERENCE)
@PartitionBy(PartitionType.NONE)
@Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
@ -95,7 +96,7 @@ import java.util.Map;
*
* @author Mark DePristo
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -71,7 +72,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities" )
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@WalkerName("FastaAlternateReferenceMaker")
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -67,7 +68,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities" )
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@WalkerName("FastaReferenceMaker")
public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -76,7 +77,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50,stop=50))
public class VariantFiltration extends RodWalker<Integer, Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -115,7 +116,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
@Reference(window=@Window(start=-200,stop=200))

3
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
@ -110,7 +111,7 @@ import java.util.*;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
public class IndelRealigner extends ReadWalker<Integer, Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -29,6 +29,7 @@ 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.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;
@ -95,7 +96,7 @@ import java.util.TreeSet;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, BadMateFilter.class, Platform454Filter.class, BadCigarFilter.class})
@Reference(window=@Window(start=-1,stop=50))
@Allows(value={DataSource.READS, DataSource.REFERENCE})

3
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
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@ -32,6 +32,7 @@ import org.apache.commons.jexl2.JexlEngine;
import org.apache.commons.jexl2.MapContext;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
@ -127,7 +128,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
// @Output

3
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -73,7 +74,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMap<Byte,Integer>> {
@ArgumentCollection

3
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -27,6 +27,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -92,7 +93,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
// Filter out all reads with zero mapping quality
@ReadFilters({MappingQualityZeroFilter.class})
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false;
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -38,7 +39,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@Output(doc="Write count to this file instead of STDOUT")
PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
@ -37,7 +38,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReads extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.validation;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -189,7 +190,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
* @since ${DATE}
*/
@DocumentedGATKFeature( groupName = "Validation Utilities" )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.READS, DataSource.REFERENCE})
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE)

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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@ -8,6 +8,7 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -89,7 +90,7 @@ import java.util.List;
* @author chartl
* @since July 2011
*/
@DocumentedGATKFeature( groupName = "Validation Utilities" )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.REFERENCE})
public class ValidationAmplicons extends RodWalker<Integer,Integer> {
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
View File

@ -24,6 +24,7 @@
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -97,7 +98,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities" )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
public enum AF_COMPUTATION_MODE {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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@ -7,6 +7,7 @@ import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -87,7 +88,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50, stop=50))
@PartitionBy(PartitionType.NONE)
public class VariantEval extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -29,6 +29,7 @@ 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.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -86,7 +87,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
public class ApplyRecalibration extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -110,7 +111,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.NONE)
public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
@ -97,7 +98,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50,stop=50))
public class CombineVariants extends RodWalker<Integer, Integer> {
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -30,6 +30,7 @@ import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -77,7 +78,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-200,stop=200))
public class LeftAlignVariants extends RodWalker<Integer, Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -187,7 +188,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
public class SelectVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -67,7 +68,7 @@ import java.util.Set;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities" )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=0,stop=100))
public class ValidateVariants extends RodWalker<Integer, Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -82,7 +83,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities" )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=0,stop=40))
public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@ -98,7 +99,7 @@ import java.util.*;
* @author Mark DePristo
* @since 2010
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
public class VariantsToTable extends RodWalker<Integer, Integer> {
/**
* Variants from this VCF file are used by this tool as input.

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -79,7 +80,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-40,stop=40))
public class VariantsToVCF extends RodWalker<Integer, Integer> {