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Refactored GATKDocs categories some more ( GSATDG-62 ) 

-- Renamed ValidatePileup to CheckPileup since validation is reserved word
-- Renamed AlignmentValidation to CheckAlignment (same as above)
-- Refactored category definitions to use constants defined in HelpConstants
-- Fixed a couple of minor typos and an example error
-- Reorganized the GATKDocs index template to use supercategories
-- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
This commit is contained in:
Geraldine Van der Auwera 2013-02-12 16:27:18 -05:00
parent 357d196dad
commit 6208742f7c
82 changed files with 245 additions and 122 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
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@ -75,7 +75,7 @@ import java.util.Map;
* over all samples. Note though that the DP is affected by downsampling (-dcov), so the max value one can obtain for
* N samples with -dcov D is N * D
*/
public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public class Coverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -55,6 +55,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -69,7 +70,7 @@ import java.util.Map;
/**
* The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -67,6 +67,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.recalibration.*;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -127,7 +128,7 @@ import java.util.List;
* </pre>
*/
@DocumentedGATKFeature(groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class})
@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class})
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
@PartitionBy(PartitionType.READ)

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
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@ -59,6 +59,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.util.HashMap;
import java.util.Map;
@ -87,7 +88,7 @@ import java.util.Map;
* @since 10/30/11
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
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;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -66,6 +66,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.BySampleSAMFileWriter;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -102,7 +103,7 @@ import java.util.*;
* </pre>
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class})
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=40)

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
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@ -262,7 +262,7 @@ public class BaseCoverageDistribution extends LocusWalker<ArrayList<Integer>, Ma
* tools to run with @By(DataSource.READS) instead of @By(DataSource.REFERENCE), while still accurately calculating
* uncovered bases
*
* //todo -- make this a generic capability of DepthOfCoverage and DiagnoseTargets
* //todo -- make this a generic capability of Coverage and DiagnoseTargets
*
* - Modifies the global variable uncoveredBases
* - Uses global variables: intervalList and previousLocus

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -56,6 +56,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -104,7 +105,7 @@ import java.util.*;
* @author Mauricio Carneiro, Roger Zurawicki
* @since 5/8/12
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@By(value = DataSource.READS)
@PartitionBy(PartitionType.INTERVAL)
public class DiagnoseTargets extends LocusWalker<Long, Long> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -59,10 +59,11 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000)
public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -62,6 +62,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -139,7 +140,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_INPUT)
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
@Reference(window=@Window(start=-200,stop=200))

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -73,6 +73,7 @@ import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -129,7 +130,7 @@ import java.util.*;
* @since 8/22/11
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionTraversalParameters(extension=65, maxRegion=300)

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
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@ -60,6 +60,7 @@ import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
@ -104,7 +105,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-HaplotypeResolver.ACTIVE_WINDOW,stop= HaplotypeResolver.ACTIVE_WINDOW))
public class HaplotypeResolver extends RodWalker<Integer, Integer> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -69,6 +69,7 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
@ -133,7 +134,7 @@ import java.util.*;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_OUTPUT)
public class IndelRealigner extends ReadWalker<Integer, Integer> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
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@ -55,6 +55,7 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -87,7 +88,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
@Output(required=false, doc="Output bam")

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -60,6 +60,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.VariantContext;
@ -117,7 +118,7 @@ import java.util.TreeSet;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, 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
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -58,6 +58,7 @@ import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -122,7 +123,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMap<Byte,Integer>> {
@ArgumentCollection

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -57,6 +57,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.BaseUtils;
@ -118,7 +119,7 @@ import static org.broadinstitute.sting.utils.variant.GATKVCFUtils.getVCFHeadersF
// Filter out all reads with zero mapping quality
@ReadFilters({MappingQualityZeroFilter.class})
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
@Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
protected boolean DEBUG = false;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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@ -57,6 +57,7 @@ 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.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
@ -212,7 +213,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
* @since ${DATE}
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.READS, DataSource.REFERENCE})
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE)

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
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@ -54,6 +54,7 @@ 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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
@ -121,7 +122,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
public enum AF_COMPUTATION_MODE {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -59,6 +59,7 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -107,7 +108,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
public class ApplyRecalibration extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -59,6 +59,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
@ -125,7 +126,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.NONE)
public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
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@ -60,6 +60,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*;
@ -98,7 +99,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class RegenotypeVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

5
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java → public/java/src/org/broadinstitute/sting/alignment/CheckAlignment.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Iterator;
@ -48,8 +49,8 @@ import java.util.Iterator;
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
public class AlignmentValidation extends ReadWalker<Integer,Integer> {
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CheckAlignment extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.
*/

2
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -50,7 +50,7 @@ import java.util.*;
* gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here,
* the gatk engine should deal with any data related information.
*/
@DocumentedGATKFeature(groupName = "GATK Engine (parameters available to all tools)")
@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_ENGINE)
public class CommandLineGATK extends CommandLineExecutable {
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
private String analysisName = null;

3
public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
View File

@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -45,7 +46,7 @@ import java.util.Map;
/**
* Computes the coverage per sample for every position (use with -L argument!).
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CoverageBySample extends LocusWalker<Integer, Integer> {
@Output
protected PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
View File

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;
@ -47,7 +48,7 @@ import java.io.PrintStream;
*
* @author aaron
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements TreeReducible<Long> {
public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;

3
public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
View File

@ -29,12 +29,13 @@ import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
/**
* A SamRecordFilter that also depends on the header.
*/
@DocumentedGATKFeature(
groupName = "Read Filters",
groupName = HelpConstants.DOCS_CAT_RF,
summary = "GATK Engine arguments that filter or transfer incoming SAM/BAM data files" )
public abstract class ReadFilter implements SamRecordFilter {
/**

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

@ -35,6 +35,7 @@ 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.annotator.interfaces.*;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
@ -71,14 +72,14 @@ import java.util.*;
* -T VariantAnnotator \
* -I input.bam \
* -o output.vcf \
* -A DepthOfCoverage \
* -A Coverage \
* --variant input.vcf \
* -L input.vcf \
* --dbsnp dbsnp.vcf
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, 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/annotator/interfaces/VariantAnnotatorAnnotation.java
View File

@ -26,13 +26,14 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.List;
import java.util.Set;
@DocumentedGATKFeature(enable = true, groupName = "Variant Annotations", summary = "Annotations available to VariantAnnotator and the variant callers (some restrictions apply)")
@DocumentedGATKFeature(enable = true, groupName = HelpConstants.DOCS_CAT_ANNOT, summary = "Annotations available to VariantAnnotator and the variant callers (some restrictions apply)")
public abstract class VariantAnnotatorAnnotation {
// return the INFO keys
public abstract List<String> getKeyNames();

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

@ -35,6 +35,7 @@ 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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -74,7 +75,7 @@ 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", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
@ArgumentCollection

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

@ -38,6 +38,7 @@ 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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFFilterHeaderLine;
@ -78,7 +79,7 @@ import java.util.*;
*
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, 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/beagle/VariantsToBeagleUnphased.java
View File

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
@ -56,7 +57,7 @@ import java.util.Set;
* in input variant file. Will additionally 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
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;

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

@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.BaseUtils;
@ -123,7 +124,7 @@ import java.io.PrintStream;
* @author Mark DePristo
* @since May 7, 2010
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, 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/CompareCallableLoci.java
View File

@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.Arrays;
@ -46,7 +47,7 @@ import java.util.List;
/**
* Test routine for new VariantContext object
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CompareCallableLoci extends RodWalker<List<CallableLoci.CallableBaseState>, long[][]> {
@Output
protected PrintStream out;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
View File

@ -50,6 +50,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.File;
import java.io.PrintStream;
@ -59,7 +60,7 @@ import java.util.*;
* Toolbox for assessing sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
*
* <p>
* DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and
* Coverage processes a set of bam files to determine coverage at different levels of partitioning and
* aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by
* sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles,
* and/or percentage of bases covered to or beyond a threshold.
@ -101,7 +102,7 @@ import java.util.*;
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T DepthOfCoverage \
* -T Coverage \
* -o file_name_base \
* -I input_bams.list
* [-geneList refSeq.sorted.txt] \
@ -116,7 +117,7 @@ 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", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, 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/coverage/GCContentByInterval.java
View File

@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.List;
@ -63,7 +64,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE})
@By(DataSource.REFERENCE)

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

@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -93,7 +94,7 @@ import java.io.PrintStream;
*
* @author Kiran Garimella, Mark DePristo
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
@Output PrintStream out;
@Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false)

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

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.Median;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
@ -97,7 +98,7 @@ import java.util.Map;
*
* @author Mark DePristo
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;

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

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
@ -71,7 +72,7 @@ import java.util.List;
* @author Kiran Garimela
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;

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

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.File;
import java.io.PrintStream;
@ -134,7 +135,7 @@ import java.util.List;
* @author Mark DePristo
* @since 7/4/11
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class DiffObjects extends RodWalker<Integer, Integer> {
/**
* Writes out a file of the DiffEngine format:

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

@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collections;
@ -81,7 +82,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_REFUTILS, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceMaker extends FastaReferenceMaker {

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

@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
@ -67,7 +68,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_REFUTILS, extraDocs = {CommandLineGATK.class} )
public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
@Output PrintStream out;

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

@ -33,13 +33,14 @@ 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.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
/**
* Calculates basic statistics about the reference sequence itself
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
@Output PrintStream out;

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

@ -37,6 +37,7 @@ 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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -78,7 +79,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50,stop=50))
public class VariantFiltration extends RodWalker<Integer, Integer> {

17
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java
View File

@ -42,6 +42,7 @@ 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.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;
@ -52,9 +53,9 @@ import java.util.Arrays;
* each overlapping read, and quality score) to the reference pileup data generated by samtools. Samtools' pileup data
* should be specified using the command-line argument '-pileup:SAMPileup <your sam pileup file>'.
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.READS,DataSource.REFERENCE})
public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
public class CheckPileup extends LocusWalker<Integer, CheckPileupStats> implements TreeReducible<CheckPileupStats> {
@Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true)
RodBinding<SAMPileupFeature> pileup;
@ -120,15 +121,15 @@ public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> impl
}
// Given result of map function
public ValidationStats reduceInit() { return new ValidationStats(); }
public ValidationStats reduce(Integer value, ValidationStats sum) {
public CheckPileupStats reduceInit() { return new CheckPileupStats(); }
public CheckPileupStats reduce(Integer value, CheckPileupStats sum) {
sum.nLoci++;
sum.nBases += value;
return sum;
}
public ValidationStats treeReduce( ValidationStats lhs, ValidationStats rhs ) {
ValidationStats combined = new ValidationStats();
public CheckPileupStats treeReduce( CheckPileupStats lhs, CheckPileupStats rhs ) {
CheckPileupStats combined = new CheckPileupStats();
combined.nLoci = lhs.nLoci + rhs.nLoci;
combined.nBases = lhs.nBases + rhs.nBases;
return combined;
@ -155,11 +156,11 @@ public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> impl
}
}
class ValidationStats {
class CheckPileupStats {
public long nLoci = 0;
public long nBases = 0;
public ValidationStats() {
public CheckPileupStats() {
}
public String toString() {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
View File

@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
@ -52,13 +53,12 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T CountBases \
* -o output.txt \
* -I input.bam \
* [-L input.intervals]
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountBases extends ReadWalker<Integer, Long> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

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

@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.Collections;
@ -48,7 +49,7 @@ import java.util.List;
* very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
* This was its very first use.
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CountIntervals extends RefWalker<Long, Long> {
@Output
PrintStream out;

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

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
@ -65,7 +66,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable {
@Output(doc="Write count to this file instead of STDOUT")
PrintStream out;

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

@ -34,12 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* Walks over the input data set, calculating the number of reads seen from male samples for diagnostic purposes.
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountMales extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

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

@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.*;
@ -73,7 +74,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>>, NanoSchedulable {
@Output
public PrintStream out;

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

@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.util.Collections;
import java.util.List;
@ -65,7 +66,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CountRODsByRef extends RefWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> {
/**

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

@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -66,7 +67,7 @@ import java.util.Map;
* </pre>
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
@Output (doc = "GATKReport table output")

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

@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
@ -63,7 +64,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReads extends ReadWalker<Integer, Integer> implements NanoSchedulable {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

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

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.List;
@ -63,7 +64,7 @@ import java.util.List;
* [-L input.intervals]
* </pre>
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

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

@ -38,12 +38,13 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
/**
* a walker that simply throws errors. Allows us to test that the engine is behaving as expected with error handling
*/
@Hidden
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_TEST, extraDocs = {CommandLineGATK.class} )
public class ErrorThrowing extends RefWalker<Integer,Integer> implements TreeReducible<Integer>, NanoSchedulable {
@Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true)
public String exceptionToThrow;

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

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
@ -72,7 +73,7 @@ import java.text.NumberFormat;
* reads with QC failure flag set, number of duplicates, percentage mapped, etc.
* @author aaron
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements NanoSchedulable {
@Output

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

@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -54,7 +55,7 @@ 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>
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class Pileup extends LocusWalker<String, Integer> implements TreeReducible<Integer>, NanoSchedulable {
private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names

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

@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
@ -42,7 +43,7 @@ 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.
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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;

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

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import java.io.PrintStream;
@ -61,7 +62,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class QCRef extends RefWalker<Integer, Integer> {
@Output
public PrintStream out;

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

@ -40,6 +40,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -56,7 +57,7 @@ import java.util.Arrays;
* Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
* of the clipping to the output stream.
*/
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
@Output

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

@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
@ -153,7 +154,7 @@ import java.util.regex.Pattern;
* @author Mark DePristo
* @since 2010
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
/**

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

@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
@ -90,7 +91,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@ReadTransformersMode(ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
@Requires({DataSource.READS, DataSource.REFERENCE})

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

@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -51,7 +52,7 @@ import java.util.Map;
* Divides the input data set into separate BAM files, one for each sample in the input data set. The split
* files are named concatenating the sample name to the end of the provided outputRoot command-line argument.
*/
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@WalkerName("SplitSamFile")
@Requires({DataSource.READS})
public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {

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

@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;
@ -116,7 +117,7 @@ import java.util.List;
* @author chartl
* @since July 2011
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.REFERENCE})
public class ValidationAmplicons extends RodWalker<Integer,Integer> {
/**

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

@ -48,6 +48,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc
import org.broadinstitute.sting.gatk.walkers.varianteval.util.VariantEvalUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
@ -114,7 +115,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, 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/variantutils/CombineVariants.java
View File

@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -113,7 +114,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-50,stop=50))
public class CombineVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
/**

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

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@ -46,7 +47,7 @@ import java.util.*;
/**
* Filters a lifted-over VCF file for ref bases that have been changed.
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=0,stop=100))
public class FilterLiftedVariants extends RodWalker<Integer, Integer> {

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

@ -39,6 +39,7 @@ 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.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@ -79,7 +80,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, 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/LiftoverVariants.java
View File

@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -55,7 +56,7 @@ import java.util.*;
/**
* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class LiftoverVariants extends RodWalker<Integer, Integer> {
@ArgumentCollection

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

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
@ -51,7 +52,7 @@ import java.util.*;
/**
* Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
@ArgumentCollection

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

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@ -104,7 +105,7 @@ import java.util.*;
* </pre>
*/
@SuppressWarnings("unused")
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class SelectHeaders extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

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

@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -178,7 +179,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, 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
View File

@ -34,6 +34,7 @@ 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.*;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -74,7 +75,7 @@ import java.util.Set;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, 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
View File

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -83,7 +84,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, 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/VariantsToBinaryPed.java
View File

@ -37,6 +37,7 @@ 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.MathUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -51,7 +52,7 @@ import java.util.*;
/**
* Converts a VCF file to a binary plink Ped file (.bed/.bim/.fam)
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=0,stop=100))
public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
@ArgumentCollection

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

@ -28,6 +28,7 @@ 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.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
@ -101,7 +102,7 @@ import java.util.*;
* @author Mark DePristo
* @since 2010
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, 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
View File

@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -82,7 +83,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-40,stop=40))
public class VariantsToVCF extends RodWalker<Integer, Integer> {

2
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -46,7 +46,7 @@ import java.io.File;
* Time: 2:24:09 PM
*/
@DocumentedGATKFeature(
groupName = "User Exceptions",
groupName = HelpConstants.DOCS_CAT_USRERR,
summary = "Errors caused by incorrect user behavior, such as bad files, bad arguments, etc." )
public class UserException extends ReviewedStingException {
/**

26
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
View File

@ -51,8 +51,8 @@ import java.util.*;
* <p/>
* This document has the following workflow:
* <p/>
* 1 -- walk the javadoc heirarchy, looking for class that have the
* DocumentedGATKFeature annotation or are in the type heirarchy in the
* 1 -- walk the javadoc hierarchy, looking for class that have the
* DocumentedGATKFeature annotation or are in the type hierarchy in the
* static list of things to document, and are to be documented
* 2 -- construct for each a GATKDocWorkUnit, resulting in the complete
* set of things to document
@ -117,7 +117,7 @@ public class GATKDoclet {
static {
STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
"ROD Codecs",
HelpConstants.DOCS_CAT_RODCODECS,
"Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED"));
}
@ -411,6 +411,8 @@ public class GATKDoclet {
}
}
//System.out.printf(groups.toString());
root.put("data", data);
root.put("groups", groups);
root.put("timestamp", buildTimestamp);
@ -421,6 +423,7 @@ public class GATKDoclet {
/**
* Trivial helper routine that returns the map of name and summary given the annotation
* AND adds a super-category so that we can custom-order the categories in the index
*
* @param annotation
* @return
@ -430,6 +433,23 @@ public class GATKDoclet {
root.put("id", annotation.groupName().replaceAll("\\W", ""));
root.put("name", annotation.groupName());
root.put("summary", annotation.summary());
/**
* Add-on super-category definitions. The assignments depend on parsing the names
* defined in HelpConstants.java so be careful of changing anything.
* Also, the super-category value strings need to be the same as used in the
* Freemarker template. This is all fairly clunky but the best I could do without
* making major changes to the DocumentedGATKFeatureObject. Doesn't help that
* Freemarker makes any scripting horribly awkward.
*/
final String supercatValue;
if (annotation.groupName().endsWith(" Tools")) supercatValue = "tools";
else if (annotation.groupName().endsWith(" Utilities")) supercatValue = "utilities";
else if (annotation.groupName().startsWith("Engine ")) supercatValue = "engine";
else supercatValue = "other";
root.put("supercat", supercatValue);
return root;
}

18
public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java
View File

@ -32,6 +32,24 @@ public class HelpConstants {
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
/**
* Definition of the group names / categories of tools.
* The names get parsed to make supercategories in the doc index,
* so be careful when making big changes -- see GATKDoclet.java toMap()
*/
public final static String DOCS_CAT_DATA = "Sequence Data Processing Tools";
public final static String DOCS_CAT_QC = "Diagnostics and Quality Control Tools";
public final static String DOCS_CAT_ENGINE = "Engine Parameters (available to all tools)";
public final static String DOCS_CAT_RF = "Read Filters";
public final static String DOCS_CAT_REFUTILS = "Reference Utilities";
public final static String DOCS_CAT_RODCODECS = "ROD Codecs";
public final static String DOCS_CAT_USRERR = "User Exceptions";
public final static String DOCS_CAT_VALIDATION = "Validation Utilities";
public final static String DOCS_CAT_ANNOT = "Variant Annotations";
public final static String DOCS_CAT_VARDISC = "Variant Discovery Tools";
public final static String DOCS_CAT_VARMANIP = "Variant Evaluation and Manipulation Tools";
public final static String DOCS_CAT_TEST = "Testing Tools";
public static String forumPost(String post) {
return GATK_FORUM_URL + post;
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java → public/java/test/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java
View File

@ -36,11 +36,11 @@ import java.util.Collections;
* @author mhanna
* @version 0.1
*/
public class ValidatingPileupIntegrationTest extends WalkerTest {
public class CheckPileupIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testEcoliThreaded() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T ValidatingPileup" +
"-T CheckPileup" +
" -I " + validationDataLocation + "MV1994.selected.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" --pileup:SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +

52
settings/helpTemplates/common.html
View File

@ -29,7 +29,8 @@
-->
<#global siteRoot = "http://www.broadinstitute.org/gatk/" />
<#global forum = "http://gatk.vanillaforums.com/" />
<#global guideIndex = "http://www.broadinstitute.org/gatk/guide/" />
<#global forum = "http://gatkforums.broadinstitute.org/" />
<#macro makeHeader title isIndex>
<?php ob_start(); ?>
@ -57,7 +58,7 @@
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container-fluid">
<a class="brand" href="index.html">GATK Documentation</a>
<a class="brand" href="index.html">GATK | Technical Documentation</a>
</div>
</div>
</div>
@ -79,9 +80,11 @@
<#macro footerInfo>
<hr>
<p class="see-also">See also <a href="index.html">Documentation index</a> | <a
href="${siteRoot}">GATK Site</a> | <a
href="${forum}">GATK support forum</a></p>
<p class="see-also">See also
<a href="${guideIndex}">Guide Index</a> |
<a href="index.html">Technical Documentation Index</a> |
<a href="${forum}">Support Forum</a>
</p>
<p class="version">GATK version ${version} built at ${timestamp}.</p>
</#macro>
@ -106,22 +109,27 @@
}
</style>
<ul class="nav nav-pills nav-stacked" id="sidenav">
<#list groups?sort_by("name") as group>
<li><a data-toggle="collapse" data-parent="#sidenav" href="#${group.id}">${group.name}</a>
<div id="${group.id}"
<?php echo ($group == '${group.name}')? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
<ul>
<#list data as datum>
<#if datum.group == group.name>
<li>
<a href="${datum.filename}">${datum.name}</a>
</li>
</#if>
</#list>
</ul>
</div>
</li>
</#list>
<#assign seq = ["engine", "tools", "utilities", "other"]>
<#list seq as supercat>
<hr>
<#list groups?sort_by("name") as group>
<#if group.supercat == supercat>
<li><a data-toggle="collapse" data-parent="#sidenav" href="#${group.id}">${group.name}</a>
<div id="${group.id}"
<?php echo ($group == '${group.name}')? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
<ul>
<#list data as datum>
<#if datum.group == group.name>
<li>
<a href="${datum.filename}">${datum.name}</a>
</li>
</#if>
</#list>
</ul>
</div>
</li>
</#if>
</#list>
</#list>
</ul>
</#macro>

17
settings/helpTemplates/generic.index.template.html
View File

@ -53,15 +53,20 @@
</div>
</#macro>
<@makeHeader title="GATK documentation index" isIndex=true />
<h1>GATK documentation index
<@makeHeader title="Technical Documentation Index" isIndex=true />
<h1>Technical Documentation Index
<small>${version}</small>
</h1>
<hr>
<div class="accordion" id="index">
<#list groups?sort_by("name") as group>
<@emitGroup group=group/>
</#list>
<#assign seq = ["engine", "tools", "utilities", "other"]>
<#list seq as supercat>
<hr>
<#list groups?sort_by("name") as group>
<#if group.supercat == supercat>
<@emitGroup group=group/>
</#if>
</#list>
</#list>
</div>
<@footerInfo />