From 6208742f7c511a45c2f9169606597eed5e2e12d8 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 12 Feb 2013 16:27:18 -0500 Subject: [PATCH] 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) --- .../{DepthOfCoverage.java => Coverage.java} | 2 +- .../gatk/walkers/annotator/GCContent.java | 3 +- .../gatk/walkers/bqsr/BaseRecalibrator.java | 3 +- .../compression/reducereads/CompareBAM.java | 3 +- .../compression/reducereads/ReduceReads.java | 3 +- .../targets/BaseCoverageDistribution.java | 2 +- .../diagnostics/targets/DiagnoseTargets.java | 3 +- .../targets/FindCoveredIntervals.java | 3 +- .../walkers/genotyper/UnifiedGenotyper.java | 3 +- .../haplotypecaller/HaplotypeCaller.java | 3 +- .../haplotypecaller/HaplotypeResolver.java | 3 +- .../gatk/walkers/indels/IndelRealigner.java | 3 +- .../gatk/walkers/indels/LeftAlignIndels.java | 3 +- .../indels/RealignerTargetCreator.java | 3 +- .../walkers/phasing/PhaseByTransmission.java | 3 +- .../walkers/phasing/ReadBackedPhasing.java | 3 +- .../validation/GenotypeAndValidate.java | 3 +- .../ValidationSiteSelector.java | 3 +- .../ApplyRecalibration.java | 3 +- .../VariantRecalibrator.java | 3 +- .../variantutils/RegenotypeVariants.java | 3 +- ...entValidation.java => CheckAlignment.java} | 5 +- .../sting/gatk/CommandLineGATK.java | 2 +- .../sting/gatk/examples/CoverageBySample.java | 3 +- .../gatk/examples/GATKPaperGenotyper.java | 3 +- .../sting/gatk/filters/ReadFilter.java | 3 +- .../walkers/annotator/VariantAnnotator.java | 5 +- .../VariantAnnotatorAnnotation.java | 3 +- .../walkers/beagle/BeagleOutputToVCF.java | 3 +- .../walkers/beagle/ProduceBeagleInput.java | 3 +- .../beagle/VariantsToBeagleUnphased.java | 3 +- .../gatk/walkers/coverage/CallableLoci.java | 3 +- .../walkers/coverage/CompareCallableLoci.java | 3 +- .../walkers/coverage/DepthOfCoverage.java | 7 +-- .../walkers/coverage/GCContentByInterval.java | 3 +- .../diagnostics/ErrorRatePerCycle.java | 3 +- .../diagnostics/ReadGroupProperties.java | 3 +- .../diagnostics/ReadLengthDistribution.java | 3 +- .../gatk/walkers/diffengine/DiffObjects.java | 3 +- .../fasta/FastaAlternateReferenceMaker.java | 3 +- .../walkers/fasta/FastaReferenceMaker.java | 3 +- .../sting/gatk/walkers/fasta/FastaStats.java | 3 +- .../walkers/filters/VariantFiltration.java | 3 +- ...ValidatingPileup.java => CheckPileup.java} | 17 +++--- .../sting/gatk/walkers/qc/CountBases.java | 4 +- .../sting/gatk/walkers/qc/CountIntervals.java | 3 +- .../sting/gatk/walkers/qc/CountLoci.java | 3 +- .../sting/gatk/walkers/qc/CountMales.java | 3 +- .../sting/gatk/walkers/qc/CountRODs.java | 3 +- .../sting/gatk/walkers/qc/CountRODsByRef.java | 3 +- .../gatk/walkers/qc/CountReadEvents.java | 3 +- .../sting/gatk/walkers/qc/CountReads.java | 3 +- .../gatk/walkers/qc/CountTerminusEvent.java | 3 +- .../sting/gatk/walkers/qc/ErrorThrowing.java | 3 +- .../sting/gatk/walkers/qc/FlagStat.java | 3 +- .../sting/gatk/walkers/qc/Pileup.java | 3 +- .../sting/gatk/walkers/qc/PrintRODs.java | 3 +- .../sting/gatk/walkers/qc/QCRef.java | 3 +- .../gatk/walkers/qc/ReadClippingStats.java | 3 +- .../gatk/walkers/readutils/ClipReads.java | 3 +- .../gatk/walkers/readutils/PrintReads.java | 3 +- .../gatk/walkers/readutils/SplitSamFile.java | 3 +- .../validation/ValidationAmplicons.java | 3 +- .../gatk/walkers/varianteval/VariantEval.java | 3 +- .../walkers/variantutils/CombineVariants.java | 3 +- .../variantutils/FilterLiftedVariants.java | 3 +- .../variantutils/LeftAlignVariants.java | 3 +- .../variantutils/LiftoverVariants.java | 3 +- .../variantutils/RandomlySplitVariants.java | 3 +- .../walkers/variantutils/SelectHeaders.java | 3 +- .../walkers/variantutils/SelectVariants.java | 3 +- .../variantutils/ValidateVariants.java | 3 +- .../VariantValidationAssessor.java | 3 +- .../variantutils/VariantsToBinaryPed.java | 3 +- .../walkers/variantutils/VariantsToTable.java | 3 +- .../walkers/variantutils/VariantsToVCF.java | 3 +- .../sting/utils/exceptions/UserException.java | 2 +- .../sting/utils/help/GATKDoclet.java | 26 ++++++++-- .../sting/utils/help/HelpConstants.java | 18 +++++++ ...t.java => CheckPileupIntegrationTest.java} | 4 +- settings/helpTemplates/common.html | 52 +++++++++++-------- .../helpTemplates/generic.index.template.html | 17 +++--- 82 files changed, 245 insertions(+), 122 deletions(-) rename protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/{DepthOfCoverage.java => Coverage.java} (99%) rename public/java/src/org/broadinstitute/sting/alignment/{AlignmentValidation.java => CheckAlignment.java} (96%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ValidatingPileup.java => CheckPileup.java} (91%) rename public/java/test/org/broadinstitute/sting/gatk/walkers/qc/{ValidatingPileupIntegrationTest.java => CheckPileupIntegrationTest.java} (94%) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java similarity index 99% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java index 4adb2ca71..5138ac9af 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java @@ -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 annotate(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index f2fc5b7ba..48b3593c5 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -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 annotate(final RefMetaDataTracker tracker, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 6a6f6d774..e1972334b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -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; * */ -@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) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java index cf1ac9d0f..a8a765ddc 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java @@ -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, 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; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index a463c847d..8e45f6db1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -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.*; * */ -@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) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java index 2b79836b9..37e82a90c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java @@ -262,7 +262,7 @@ public class BaseCoverageDistribution extends LocusWalker, 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 diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java index 8f1626bd7..8b9b37c18 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java @@ -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 { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index fd9ad30ce..09cdee22b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -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 { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 12cd7061e..137a1cfa5 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -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)) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 5c8b84bdd..a8996c980 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -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) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java index 73b8f8524..c7cc84b9c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java @@ -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.*; * * */ -@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 { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 928aa57ab..596f2341b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -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 { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 6eb2a633c..ff21893f1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -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; * * */ -@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) public class LeftAlignIndels extends ReadWalker { @Output(required=false, doc="Output bam") diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 4d8dda34a..dea17cd02 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -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}) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 80c49ff19..21f2bd8db 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -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.*; * * */ -@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class PhaseByTransmission extends RodWalker, HashMap> { @ArgumentCollection diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index fe38461c5..e8388a3d7 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -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 { @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; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index f0efb3cd9..d6a814ee8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -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) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index ce44f546d..5c216928b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -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.*; * * */ -@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} ) public class ValidationSiteSelector extends RodWalker { public enum AF_COMPUTATION_MODE { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 279e5f218..f2120213a 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -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 implements TreeReducible { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index d8d79e26c..57d9c219c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -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> implements TreeReducible> { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java index c8fc27e6a..85d25aecf 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java @@ -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.*; * * */ -@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class RegenotypeVariants extends RodWalker implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/CheckAlignment.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java rename to public/java/src/org/broadinstitute/sting/alignment/CheckAlignment.java index e2b5037d0..93b4d5e6f 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java +++ b/public/java/src/org/broadinstitute/sting/alignment/CheckAlignment.java @@ -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 { +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) +public class CheckAlignment extends ReadWalker { /** * The supporting BWT index generated using BWT. */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index d19245476..5fc0ccd3e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java index b44406c81..c96fe564c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java @@ -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 { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java index df25ccdad..7b56852d3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java @@ -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 implements TreeReducible { public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index b2fc8dd6f..2387312b9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -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 { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index b03b5327f..826dc9f22 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -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 * * */ -@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)) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 5c8d76904..f640c99c8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -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 getKeyNames(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 09b2cba80..2e85fe8f9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -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;

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

*/ -@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class BeagleOutputToVCF extends RodWalker { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index 15527d34a..937c3abc0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -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 { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index 3ef688d02..ab0ce79fd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -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 { @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 564a046da..0681ebf1e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -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 { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index ac84277d8..3844db38c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -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, long[][]> { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java index d9e5e3e98..3bd114aa1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java @@ -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 * *

- * 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.*; * 

  * 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)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
index 257386232..9a6ef61d8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
@@ -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;
  *
* */ -@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) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 10b02ac7d..f361d5e2b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -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 { @Output PrintStream out; @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java index b8bd12e87..de7ac3e41 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java @@ -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 { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java index 4bf0a05ca..ccad7f0b2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java @@ -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 { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java index e93732681..d1903c2bb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java @@ -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 { /** * Writes out a file of the DiffEngine format: diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java index 582a8304b..e881315b9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java @@ -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; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java index 84a2025ec..f2f5fb5fe 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java @@ -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; * * */ -@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_REFUTILS, extraDocs = {CommandLineGATK.class} ) public class FastaReferenceMaker extends RefWalker, GenomeLoc> { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java index 0862043bf..9fbaca14e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java @@ -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 { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java index 091d5e428..61a847f4c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java @@ -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.*; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java similarity index 91% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java index 40209a8d7..533c7be73 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java @@ -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 '. */ -@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 implements TreeReducible { +public class CheckPileup extends LocusWalker implements TreeReducible { @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true) RodBinding pileup; @@ -120,15 +121,15 @@ public class ValidatingPileup extends LocusWalker 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 impl } } -class ValidationStats { +class CheckPileupStats { public long nLoci = 0; public long nBases = 0; - public ValidationStats() { + public CheckPileupStats() { } public String toString() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java index b44620c53..503cdb6d6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java @@ -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] * * */ -@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 { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java index c96eb7b6f..3b8eba398 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java @@ -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 { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java index 9a3dccd70..f2bd791c1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java @@ -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; * * */ -@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class CountLoci extends LocusWalker implements TreeReducible, NanoSchedulable { @Output(doc="Write count to this file instead of STDOUT") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java index 3a3f21413..6fb4b84d6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java @@ -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 { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java index 4cb60db92..c01a1df89 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java @@ -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.*; * * */ -@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class CountRODs extends RodWalker, Long>> implements TreeReducible, Long>>, NanoSchedulable { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java index 7c392716a..303f1704f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java @@ -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; * * */ -@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class CountRODsByRef extends RefWalker, Long>> { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index b07729cf9..8b0646092 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -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; * */ -@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>> { @Output (doc = "GATKReport table output") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index ed5868b31..1a3984014 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -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; * * */ -@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 implements NanoSchedulable { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index bd3a9425c..40b78588f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -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] * */ -@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> { public Pair map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java index f4156f395..7ec93e582 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java @@ -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 implements TreeReducible, NanoSchedulable { @Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true) public String exceptionToThrow; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java index 902281eb4..d0a3f3508 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java @@ -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 implements NanoSchedulable { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java index 322ba617c..0790f2ced 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java @@ -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] */ -@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class Pileup extends LocusWalker implements TreeReducible, NanoSchedulable { private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java index b702f50f9..aada50daa 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java @@ -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 { @Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true) public RodBinding input; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index 3499c6a99..395945f03 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -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; * * */ -@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) public class QCRef extends RefWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index 5f521c355..cc8b3401e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -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 { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java index 360b508ee..f7b125828 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java @@ -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 { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java index b5a74981c..322d9425c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java @@ -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.*; * * */ -@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}) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java index 65bda82da..c64924f09 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java @@ -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> { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 78c55d1c4..45c5fe090 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -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 { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index e24c725a6..a3e480bd0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -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.*; * * */ -@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 implements TreeReducible { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 0d87bb921..e5fe46a07 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -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.*; * * */ -@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 implements TreeReducible { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index c2785e920..f285fb797 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 95c42a336..65ec7a4f0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -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.*; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index b78038953..0a7ad5b7b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -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 { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 896f36e6c..6948c4f3c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -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 { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java index e4d182d13..17aaa7513 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -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.*; * */ @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 implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 4d30408d8..9c209ae2c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -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.*; * * */ -@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class SelectVariants extends RodWalker implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 4b9f2c6c1..a242f9310 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -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; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 5bf5b96e3..02089eb6c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -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.*; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 3bd95d9ec..ce9e28c4b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -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 { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index f6c02592d..b12f51a1e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -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 { /** * Variants from this VCF file are used by this tool as input. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index a51014114..ffe61f76d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -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.*; * * */ -@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 { diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 715dd3fcd..5c67c899c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -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 { /** diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java index e119c7f08..f63a9162b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -51,8 +51,8 @@ import java.util.*; *

* This document has the following workflow: *

- * 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; } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java index 8a159b067..8edf83252 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java @@ -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; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java similarity index 94% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java index 2983d8544..4d3741228 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java @@ -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" + diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html index 45148bda6..677fdf861 100644 --- a/settings/helpTemplates/common.html +++ b/settings/helpTemplates/common.html @@ -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> @@ -57,7 +58,7 @@

- GATK Documentation + GATK | Technical Documentation
@@ -79,9 +80,11 @@ <#macro footerInfo>
-

See also Documentation index | GATK Site | GATK support forum

+

See also + Guide Index | + Technical Documentation Index | + Support Forum +

GATK version ${version} built at ${timestamp}.

@@ -106,22 +109,27 @@ } \ No newline at end of file diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html index bb4aebae5..b3e3d0212 100644 --- a/settings/helpTemplates/generic.index.template.html +++ b/settings/helpTemplates/generic.index.template.html @@ -53,15 +53,20 @@ -<@makeHeader title="GATK documentation index" isIndex=true /> -

GATK documentation index +<@makeHeader title="Technical Documentation Index" isIndex=true /> +

Technical Documentation Index ${version}

-
- <#list groups?sort_by("name") as group> - <@emitGroup group=group/> - + <#assign seq = ["engine", "tools", "utilities", "other"]> + <#list seq as supercat> +
+ <#list groups?sort_by("name") as group> + <#if group.supercat == supercat> + <@emitGroup group=group/> + + +
<@footerInfo />