From 116885a450a85c7e10dfc22983aff154838baa9a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Jul 2012 16:33:29 -0400 Subject: [PATCH] Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats. --- ivy.xml | 3 + ...{CompareBAMWalker.java => CompareBAM.java} | 2 +- .../reducereads/MultiSampleCompressor.java | 2 +- ...educeReadsWalker.java => ReduceReads.java} | 2 +- .../reducereads/SingleSampleCompressor.java | 4 +- .../reducereads/SlidingWindow.java | 4 +- .../haplotypecaller/HaplotypeCaller.java | 22 +- ...onWalker.java => AlignmentValidation.java} | 2 +- ...tsWalker.java => CountBestAlignments.java} | 2 +- .../broadinstitute/sting/gatk/Categorize.java | 38 + .../broadinstitute/sting/gatk/Category.java | 68 ++ .../gatk/executive/LinearMicroScheduler.java | 1 - .../traversals/TraverseActiveRegions.java | 28 +- .../gatk/walkers/ActiveRegionWalker.java | 3 +- .../{ClipReadsWalker.java => ClipReads.java} | 2 +- ...mesWalker.java => FindReadsWithNames.java} | 2 +- .../{FlagStatWalker.java => FlagStat.java} | 6 +- .../{PileupWalker.java => Pileup.java} | 2 +- .../{PrintRODsWalker.java => PrintRODs.java} | 2 +- ...{PrintReadsWalker.java => PrintReads.java} | 2 +- ...itSamFileWalker.java => SplitSamFile.java} | 4 +- .../gatk/walkers/annotator/AlleleBalance.java | 4 +- .../annotator/AlleleBalanceBySample.java | 8 +- .../gatk/walkers/annotator/BaseCounts.java | 4 +- .../walkers/annotator/ChromosomeCounts.java | 13 +- .../walkers/annotator/DepthOfCoverage.java | 4 +- .../annotator/DepthPerAlleleBySample.java | 12 +- .../gatk/walkers/annotator/FisherStrand.java | 4 +- .../gatk/walkers/annotator/GCContent.java | 4 +- .../walkers/annotator/HaplotypeScore.java | 4 +- .../gatk/walkers/annotator/HardyWeinberg.java | 4 +- .../walkers/annotator/HomopolymerRun.java | 5 +- .../walkers/annotator/InbreedingCoeff.java | 6 +- .../gatk/walkers/annotator/IndelType.java | 4 +- .../sting/gatk/walkers/annotator/LowMQ.java | 5 +- .../walkers/annotator/MVLikelihoodRatio.java | 4 +- .../walkers/annotator/MappingQualityZero.java | 4 +- .../annotator/MappingQualityZeroBySample.java | 4 +- .../annotator/MappingQualityZeroFraction.java | 4 +- .../gatk/walkers/annotator/NBaseCount.java | 4 +- .../gatk/walkers/annotator/QualByDepth.java | 4 +- .../walkers/annotator/RMSMappingQuality.java | 4 +- .../gatk/walkers/annotator/RankSumTest.java | 5 +- .../gatk/walkers/annotator/SampleList.java | 4 +- .../sting/gatk/walkers/annotator/SnpEff.java | 6 +- .../walkers/annotator/SpanningDeletions.java | 4 +- .../annotator/TandemRepeatAnnotator.java | 5 +- .../annotator/TechnologyComposition.java | 4 +- .../TransmissionDisequilibriumTest.java | 4 +- .../walkers/annotator/VariantAnnotator.java | 4 +- .../annotator/VariantAnnotatorEngine.java | 6 +- ...leWalker.java => AnnotatorCompatible.java} | 2 +- .../interfaces/GenotypeAnnotation.java | 3 +- .../interfaces/InfoFieldAnnotation.java | 2 +- .../VariantAnnotatorAnnotation.java | 2 +- ...oVCFWalker.java => BeagleOutputToVCF.java} | 6 +- ...putWalker.java => ProduceBeagleInput.java} | 9 +- ...ker.java => VariantsToBeagleUnphased.java} | 6 +- ...ualityScoreRecalibrator.java => BQSR.java} | 4 +- .../bqsr/StandardRecalibrationEngine.java | 2 +- ...lableLociWalker.java => CallableLoci.java} | 2 +- ...ciWalker.java => CompareCallableLoci.java} | 34 +- ...verageWalker.java => DepthOfCoverage.java} | 8 +- ...alWalker.java => GCContentByInterval.java} | 2 +- .../targets/FindCoveredIntervals.java | 3 +- ...iffObjectsWalker.java => DiffObjects.java} | 2 +- ...lker.java => FastaAlternateReference.java} | 2 +- ...ferenceWalker.java => FastaReference.java} | 2 +- ...{FastaStatsWalker.java => FastaStats.java} | 12 +- ...tionWalker.java => VariantFiltration.java} | 8 +- .../walkers/genotyper/UnifiedGenotyper.java | 6 +- ...rWalker.java => SomaticIndelDetector.java} | 5 +- .../gatk/walkers/phasing/PhasingUtils.java | 4 +- ...singWalker.java => ReadBackedPhasing.java} | 4 +- ...{CountBasesWalker.java => CountBases.java} | 2 +- .../{CountLociWalker.java => CountLoci.java} | 2 +- ...{CountMalesWalker.java => CountMales.java} | 2 +- .../{CountRODsWalker.java => CountRODs.java} | 2 +- ...DsByRefWalker.java => CountRODsByRef.java} | 8 +- ...EventsWalker.java => CountReadEvents.java} | 2 +- ...{CountReadsWalker.java => CountReads.java} | 2 +- ...entWalker.java => CountTerminusEvent.java} | 2 +- ...leQualityWalker.java => CycleQuality.java} | 2 +- ...ThrowingWalker.java => ErrorThrowing.java} | 2 +- .../qc/{QCRefWalker.java => QCRef.java} | 11 +- ...tatsWalker.java => ReadClippingStats.java} | 2 +- ...idationWalker.java => ReadValidation.java} | 2 +- ...onWalker.java => RodSystemValidation.java} | 3 +- ...ileupWalker.java => ValidatingPileup.java} | 9 +- ...teWalker.java => GenotypeAndValidate.java} | 4 +- ...alker.java => ValidationSiteSelector.java} | 8 +- ...ariantEvalWalker.java => VariantEval.java} | 3 +- .../MendelianViolationEvaluator.java | 4 +- .../evaluators/VariantEvaluator.java | 10 +- .../evaluators/VariantSummary.java | 4 +- .../stratifications/VariantStratifier.java | 8 +- .../varianteval/util/EvaluationContext.java | 14 +- .../varianteval/util/VariantEvalUtils.java | 10 +- .../sting/utils/help/GATKDocUtils.java | 15 +- .../sting/utils/help/GATKDocWorkUnit.java | 48 +- .../sting/utils/help/GATKDoclet.java | 254 ++++-- .../help/GenericDocumentationHandler.java | 215 +++--- .../gatk/GenomeAnalysisEngineUnitTest.java | 4 +- .../sting/gatk/WalkerManagerUnitTest.java | 7 +- .../reads/GATKWalkerBenchmark.java | 10 +- .../traversals/TraverseReadsUnitTest.java | 15 +- .../gatk/walkers/PrintReadsUnitTest.java | 4 +- .../VariantEvalWalkerUnitTest.java | 4 +- public/packages/GATK-Picard.xml | 12 +- settings/helpTemplates/bootstrap.min.css | 727 ++++++++++++++++++ settings/helpTemplates/bootstrap.min.js | 7 + settings/helpTemplates/common.html | 156 +++- .../helpTemplates/generic.index.template.html | 74 +- settings/helpTemplates/generic.template.html | 227 +++--- settings/helpTemplates/jquery.min.js | 4 + 115 files changed, 1807 insertions(+), 576 deletions(-) rename protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/{CompareBAMWalker.java => CompareBAM.java} (98%) rename protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/{ReduceReadsWalker.java => ReduceReads.java} (99%) rename public/java/src/org/broadinstitute/sting/alignment/{AlignmentValidationWalker.java => AlignmentValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/alignment/{CountBestAlignmentsWalker.java => CountBestAlignments.java} (98%) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/Categorize.java create mode 100644 public/java/src/org/broadinstitute/sting/gatk/Category.java rename public/java/src/org/broadinstitute/sting/gatk/walkers/{ClipReadsWalker.java => ClipReads.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{FindReadsWithNamesWalker.java => FindReadsWithNames.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{FlagStatWalker.java => FlagStat.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PileupWalker.java => Pileup.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PrintRODsWalker.java => PrintRODs.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PrintReadsWalker.java => PrintReads.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{SplitSamFileWalker.java => SplitSamFile.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/{AnnotatorCompatibleWalker.java => AnnotatorCompatible.java} (93%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{BeagleOutputToVCFWalker.java => BeagleOutputToVCF.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{ProduceBeagleInputWalker.java => ProduceBeagleInput.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{VariantsToBeagleUnphasedWalker.java => VariantsToBeagleUnphased.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/{BaseQualityScoreRecalibrator.java => BQSR.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{CallableLociWalker.java => CallableLoci.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{CompareCallableLociWalker.java => CompareCallableLoci.java} (74%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{DepthOfCoverageWalker.java => DepthOfCoverage.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{GCContentByIntervalWalker.java => GCContentByInterval.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/{DiffObjectsWalker.java => DiffObjects.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaAlternateReferenceWalker.java => FastaAlternateReference.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaReferenceWalker.java => FastaReference.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaStatsWalker.java => FastaStats.java} (87%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/filters/{VariantFiltrationWalker.java => VariantFiltration.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/indels/{SomaticIndelDetectorWalker.java => SomaticIndelDetector.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/{ReadBackedPhasingWalker.java => ReadBackedPhasing.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountBasesWalker.java => CountBases.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountLociWalker.java => CountLoci.java} (94%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountMalesWalker.java => CountMales.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountRODsWalker.java => CountRODs.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountRODsByRefWalker.java => CountRODsByRef.java} (90%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountReadEventsWalker.java => CountReadEvents.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountReadsWalker.java => CountReads.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountTerminusEventWalker.java => CountTerminusEvent.java} (96%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CycleQualityWalker.java => CycleQuality.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ErrorThrowingWalker.java => ErrorThrowing.java} (96%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{QCRefWalker.java => QCRef.java} (90%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ReadClippingStatsWalker.java => ReadClippingStats.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ReadValidationWalker.java => ReadValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{RodSystemValidationWalker.java => RodSystemValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ValidatingPileupWalker.java => ValidatingPileup.java} (94%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/validation/{GenotypeAndValidateWalker.java => GenotypeAndValidate.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/{ValidationSiteSelectorWalker.java => ValidationSiteSelector.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{VariantEvalWalker.java => VariantEval.java} (99%) create mode 100755 settings/helpTemplates/bootstrap.min.css create mode 100644 settings/helpTemplates/bootstrap.min.js create mode 100644 settings/helpTemplates/jquery.min.js diff --git a/ivy.xml b/ivy.xml index 5a8c3986a..a96567889 100644 --- a/ivy.xml +++ b/ivy.xml @@ -100,6 +100,9 @@ + + + diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java similarity index 98% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java index 3e07295e7..f8c9c5396 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java @@ -40,7 +40,7 @@ import java.util.Map; */ @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) -public class CompareBAMWalker extends LocusWalker, CompareBAMWalker.TestResults> { +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; @Argument(required = false, shortName = "teq", fullName = "test_equal_bases", doc = "Test if the bases marked as '=' are indeed ref bases.") public boolean TEST_EQUAL_BASES = false; @Argument(required = false, shortName = "tbc", fullName = "test_base_counts", doc = "Test if the base counts tag in consensus reads are accurate.") public boolean TEST_BASE_COUNTS = false; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java index 0ac9630c2..44971ca38 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java @@ -53,7 +53,7 @@ public class MultiSampleCompressor implements Compressor { final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, final int minBaseQual, - final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) { + final ReduceReads.DownsampleStrategy downsampleStrategy) { for ( String name : SampleUtils.getSAMFileSamples(header) ) { compressorsPerSample.put(name, new SingleSampleCompressor(name, contextSize, downsampleCoverage, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java similarity index 99% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 1b11cbd4e..d793ae159 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -83,7 +83,7 @@ import java.util.*; @PartitionBy(PartitionType.INTERVAL) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class}) -public class ReduceReadsWalker extends ReadWalker, ReduceReadsStash> { +public class ReduceReads extends ReadWalker, ReduceReadsStash> { @Output protected StingSAMFileWriter out; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java index fd0dfa1ff..6d2c2d215 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java @@ -26,7 +26,7 @@ public class SingleSampleCompressor implements Compressor { protected double minIndelProportionToTriggerVariant; protected int minBaseQual; - protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy; + protected ReduceReads.DownsampleStrategy downsampleStrategy; public SingleSampleCompressor(final String sampleName, final int contextSize, @@ -35,7 +35,7 @@ public class SingleSampleCompressor implements Compressor { final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, final int minBaseQual, - final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) { + final ReduceReads.DownsampleStrategy downsampleStrategy) { this.sampleName = sampleName; this.contextSize = contextSize; this.downsampleCoverage = downsampleCoverage; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java index 68dfd041b..60d7096a3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java @@ -53,7 +53,7 @@ public class SlidingWindow { protected int MIN_BASE_QUAL_TO_COUNT; // qual has to be greater than or equal to this value protected int MIN_MAPPING_QUALITY; - protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy; + protected ReduceReads.DownsampleStrategy downsampleStrategy; private boolean hasIndelQualities; /** @@ -82,7 +82,7 @@ public class SlidingWindow { } - public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReadsWalker.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) { + public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) { this.stopLocation = -1; this.contextSize = contextSize; this.downsampleCoverage = downsampleCoverage; 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 bda94cc8f..546f53002 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -33,20 +33,21 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.filters.*; +import org.broadinstitute.sting.gatk.filters.BadMateFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; +import org.broadinstitute.sting.gatk.walkers.PartitionBy; +import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; @@ -56,6 +57,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.FileNotFoundException; import java.io.PrintStream; @@ -90,7 +92,7 @@ import java.util.*; @PartitionBy(PartitionType.LOCUS) @ActiveRegionExtension(extension=65, maxRegion=275) -public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatibleWalker { +public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatible { /** * A raw, unfiltered, highly specific callset in VCF format. @@ -361,7 +363,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem //--------------------------------------------------------------------------------------------------------------- @Override - public Integer map( final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { + public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { final ArrayList activeAllelesToGenotype = new ArrayList(); @@ -476,7 +478,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // //--------------------------------------------------------------------------------------------------------------- - private void finalizeActiveRegion( final ActiveRegion activeRegion ) { + private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getExtendedLoc() + " with " + activeRegion.size() + " reads:"); } final ArrayList finalizedReadList = new ArrayList(); final FragmentCollection fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) ); @@ -503,7 +505,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem } } - private List filterNonPassingReads( final ActiveRegion activeRegion ) { + private List filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { final ArrayList readsToRemove = new ArrayList(); for( final GATKSAMRecord rec : activeRegion.getReads() ) { if( rec.getReadLength() < 24 || rec.getMappingQuality() <= 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) { @@ -514,7 +516,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem return readsToRemove; } - private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) { + private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { final int padLeft = Math.max(activeRegion.getReferenceLoc().getStart()-REFERENCE_PADDING, 1); final int padRight = Math.min(activeRegion.getReferenceLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReferenceLoc().getContig()).getSequenceLength()); return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReferenceLoc().getContig(), padLeft, padRight); diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java rename to public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index a342cf932..7af83d14b 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -46,7 +46,7 @@ import java.util.Iterator; * @author mhanna * @version 0.1 */ -public class AlignmentValidationWalker extends ReadWalker { +public class AlignmentValidation extends ReadWalker { /** * The supporting BWT index generated using BWT. */ diff --git a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java rename to public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java index d91b83e7a..b0580fe50 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java +++ b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java @@ -48,7 +48,7 @@ import java.util.TreeMap; * @author mhanna * @version 0.1 */ -public class CountBestAlignmentsWalker extends ReadWalker { +public class CountBestAlignments extends ReadWalker { /** * The supporting BWT index generated using BWT. */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/Categorize.java b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java new file mode 100644 index 000000000..b8a222983 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java @@ -0,0 +1,38 @@ +/* + * Copyright (c) 2012, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk; + +import java.lang.annotation.*; + +/** + * Allows the walker to be tagged, they can have an unlimited number of categories. + */ +@Documented +@Inherited +@Retention(RetentionPolicy.RUNTIME) +@Target(ElementType.TYPE) +public @interface Categorize { + public Category[] value() default {Category.UNCATEGORIZED}; +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/Category.java b/public/java/src/org/broadinstitute/sting/gatk/Category.java new file mode 100644 index 000000000..d1f890f95 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/Category.java @@ -0,0 +1,68 @@ +/* + * Copyright (c) 2012, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk; + +public enum Category { + + BAM_PROCESSING("Walker", "BAM Processing and Analysis Tools"), + + COMPANION("Walker", "Companion Utilities"), + + CANCER_SPECIFIC("Walker", "Cancer-specific Variant Discovery Tools"), + + QUALITY_CONTROL("Walker", "Quality Control and Simple Analysis Tools"), + + VALIDATION("Walker", "Validation Utilities"), + + VARIANT_DETECTION("ex", "Variant Detection"), + + VARIANT_DISCOVERY("Walker", "Variant Discovery Tools"), + + VARIANT_EVALUATION("Walker", "Variant Evaluation and Manipulation Tools"), + + EXPERIMENTAL("Walker", "Miscellaneous Experimental (and Potentially Unstable) Tools"), + + UNCATEGORIZED("all", "No category"); + + private final String description; + + /** + * Accepted strings are from the GATKDocWorkUnit.group + */ + private final String type; + + private Category(String type, String description) { + this.description = description; + this.type = type; + } + + public String type() { + return type; + } + + public String getDescription() { + return description; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 16487054b..b35abb775 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.DirectOutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.SampleUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index 6d0ec0e7c..1b9c12fb0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -6,10 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.providers.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActivityProfile; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -28,7 +30,7 @@ public class TraverseActiveRegions extends TraversalEngine workQueue = new LinkedList(); + private final LinkedList workQueue = new LinkedList(); private final LinkedHashSet myReads = new LinkedHashSet(); @Override @@ -109,18 +111,18 @@ public class TraverseActiveRegions extends TraversalEngine activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize ); + final List activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize ); // add active regions to queue of regions to process // first check if can merge active regions over shard boundaries if( !activeRegions.isEmpty() ) { if( !workQueue.isEmpty() ) { - final ActiveRegion last = workQueue.getLast(); - final ActiveRegion first = activeRegions.get(0); + final org.broadinstitute.sting.utils.activeregion.ActiveRegion last = workQueue.getLast(); + final org.broadinstitute.sting.utils.activeregion.ActiveRegion first = activeRegions.get(0); if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= maxRegionSize ) { workQueue.removeLast(); activeRegions.remove(first); - workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) ); + workQueue.add( new org.broadinstitute.sting.utils.activeregion.ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) ); } } workQueue.addAll( activeRegions ); @@ -183,7 +185,7 @@ public class TraverseActiveRegions extends TraversalEngine walker ) { // Just want to output the active regions to a file, not actually process them - for( final ActiveRegion activeRegion : workQueue ) { + for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) { if( activeRegion.isActive ) { walker.activeRegionOutStream.println( activeRegion.getLocation() ); } @@ -196,7 +198,7 @@ public class TraverseActiveRegions extends TraversalEngine extends TraversalEngine reads, final Queue workQueue, final T sum, final ActiveRegionWalker walker ) { + private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet reads, final Queue workQueue, final T sum, final ActiveRegionWalker walker ) { final ArrayList placedReads = new ArrayList(); for( final GATKSAMRecord read : reads ) { final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read ); if( activeRegion.getLocation().overlapsP( readLoc ) ) { // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region) long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc ); - ActiveRegion bestRegion = activeRegion; - for( final ActiveRegion otherRegionToTest : workQueue ) { + org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion; + for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) { if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) { maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc ); bestRegion = otherRegionToTest; @@ -227,7 +229,7 @@ public class TraverseActiveRegions extends TraversalEngine extends Walker { +public class ClipReads extends ReadWalker { /** * If provided, ClipReads will write summary statistics about the clipping operations applied * to the reads to this file. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java index 7f9269725..f6f091cfc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java @@ -49,7 +49,7 @@ import java.util.Set; */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @Requires({DataSource.READS, DataSource.REFERENCE}) -public class FindReadsWithNamesWalker extends ReadWalker { +public class FindReadsWithNames extends ReadWalker { /** an optional argument to dump the reads out to a BAM file */ @Output(doc="Write output to this BAM filename instead of STDOUT") SAMFileWriter out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java index 0777037bf..e5f77018c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java @@ -42,12 +42,12 @@ import java.text.NumberFormat; * @author aaron */ @Requires({DataSource.READS}) -public class FlagStatWalker extends ReadWalker { +public class FlagStat extends ReadWalker { @Output PrintStream out; // what comes out of the flagstat - static class FlagStat { + static class FlagStatus { long readCount = 0L; long QC_failure = 0L; long duplicates = 0L; @@ -117,7 +117,7 @@ public class FlagStatWalker extends ReadWalker { } - private FlagStat myStat = new FlagStat(); + private FlagStatus myStat = new FlagStatus(); public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) { myStat.readCount++; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java index b3062c546..12b575760 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java @@ -60,7 +60,7 @@ import java.util.List; * Associated command: * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] */ -public class PileupWalker extends LocusWalker implements TreeReducible { +public class Pileup extends LocusWalker implements TreeReducible { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java index 7960f5c35..cfc096ea2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java @@ -39,7 +39,7 @@ import java.io.PrintStream; * Prints out all of the RODs in the input data set. Data is rendered using the toString() method * of the given ROD. */ -public class PrintRODsWalker extends RodWalker { +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/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java index 4159a67b7..6e9960f3a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java @@ -90,7 +90,7 @@ import java.util.TreeSet; */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @Requires({DataSource.READS, DataSource.REFERENCE}) -public class PrintReadsWalker extends ReadWalker { +public class PrintReads extends ReadWalker { @Output(doc="Write output to this BAM filename instead of STDOUT", required = true) SAMFileWriter out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java index baaaf9e28..e0ee072fe 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java @@ -47,14 +47,14 @@ import java.util.Map; */ @WalkerName("SplitSamFile") @Requires({DataSource.READS}) -public class SplitSamFileWalker extends ReadWalker> { +public class SplitSamFile extends ReadWalker> { @Argument(fullName="outputRoot", doc="output BAM file", required=false) public String outputRoot = null; @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false) public Integer BAMcompression = 5; - private static Logger logger = Logger.getLogger(SplitSamFileWalker.class); + private static Logger logger = Logger.getLogger(SplitSamFile.class); private static String VERSION = "0.0.1"; public void initialize() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index dc589699a..30f81b20c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -51,7 +51,7 @@ public class AlleleBalance extends InfoFieldAnnotation { char[] BASES = {'A','C','G','T'}; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index fd23fb8f6..11c9c3a99 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.MathUtils; @@ -14,7 +14,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; /** @@ -22,7 +24,7 @@ import java.util.*; */ public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { - public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) { + public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) { Double ratio = annotateSNP(stratifiedContext, vc, g); if (ratio == null) return; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index 46aa6d0f3..c3b6de65a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -34,7 +34,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -52,7 +52,7 @@ import java.util.Map; */ public class BaseCounts extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 3d07e3a7a..54837baad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -29,18 +29,17 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -62,14 +61,14 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn private Set founderIds = new HashSet(); - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( ! vc.hasGenotypes() ) return null; return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap(), true,founderIds); } - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ){ + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ){ //If families were given, get the founders ids founderIds = ((Walker)walker).getSampleDB().getFounderIds(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index b36de0dac..28ca77f18 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; @@ -38,7 +38,7 @@ import java.util.Map; */ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index d56daadea..523aa81b1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -3,10 +3,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.Allele; @@ -14,7 +16,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; /** @@ -42,7 +46,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time - public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) { + public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) { if ( g == null || !g.isCalled() ) return; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 6dc0ba3e1..4669cfef8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; @@ -55,7 +55,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat private static final String FS = "FS"; private static final double MIN_PVALUE = 1E-320; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isVariant() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 11a64b49f..263320d1b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; @@ -22,7 +22,7 @@ import java.util.Map; */ public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { double content = computeGCContent(ref); Map map = new HashMap(); map.put(getKeyNames().get(0), String.format("%.2f", content)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 606de1b88..45444e05d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -28,7 +28,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; @@ -60,7 +60,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50; private final static char REGEXP_WILDCARD = '.'; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 795cdbeb5..6ba85de07 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -4,7 +4,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.sting.utils.QualityUtils; @@ -29,7 +29,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress private static final int MIN_GENOTYPE_QUALITY = 10; private static final int MIN_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { final GenotypesContext genotypes = vc.getGenotypes(); if ( genotypes == null || genotypes.size() < MIN_SAMPLES ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 7c4b0b42e..9f20bf375 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; @@ -23,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation { private boolean ANNOTATE_INDELS = true; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isBiallelic() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index 0d2b3478d..fa3a7459b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java @@ -3,9 +3,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; @@ -33,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno private static final int MIN_SAMPLES = 10; private Set founderIds; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { //If available, get the founder IDs and cache them. the IC will only be computed on founders then. if(founderIds == null) founderIds = ((Walker)walker).getSampleDB().getFounderIds(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java index e0abfcf3c..babaf7ee6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.IndelUtils; @@ -18,7 +18,7 @@ import java.util.*; */ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { int run; if (vc.isMixed()) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index 4651782ef..7f5033adf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -3,12 +3,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; @@ -22,7 +21,7 @@ import java.util.Map; */ public class LowMQ extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index 07fbfc3d2..b6f24433e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.gatk.samples.SampleDB; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; @@ -32,7 +32,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment private String fatherId; private String childId; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( mendelianViolation == null ) { if (checkAndSetSamples(((Walker) walker).getSampleDB())) { mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 780206f30..372d5bc9e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; @@ -24,7 +24,7 @@ import java.util.Map; */ public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index c12923be5..b5252f15b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; @@ -47,7 +47,7 @@ import java.util.List; */ public class MappingQualityZeroBySample extends GenotypeAnnotation { public void annotate(RefMetaDataTracker tracker, - AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context, + AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g, GenotypeBuilder gb) { if ( g == null || !g.isCalled() ) return; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java index e8490959c..9f542e3bd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -22,7 +22,7 @@ import java.util.Map; */ public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 8f0bc876a..ba4303b4a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -20,7 +20,7 @@ import java.util.Map; * The number of N bases, counting only SOLiD data */ public class NBaseCount extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 5da6492a6..b62cd374b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -28,7 +28,7 @@ import java.util.Map; */ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.hasLog10PError() || stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index fb5767b34..842fde8ad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; @@ -29,7 +29,7 @@ import java.util.Map; */ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index 1955c87b8..bf6adcfac 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -4,9 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.QualityUtils; @@ -32,7 +31,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR static final double INDEL_LIKELIHOOD_THRESH = 0.1; static final boolean DEBUG = false; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if (stratifiedContexts.size() == 0) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index cbf536e4f..7e4d44cf2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -46,7 +46,7 @@ import java.util.Map; */ public class SampleList extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( vc.isMonomorphicInSamples() || !vc.hasGenotypes() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 6c860fce6..4d990e738 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.utils.Utils; @@ -203,7 +203,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio } } - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ) { + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { // Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff // without providing a SnpEff rod via --snpEffFile): validateRodBinding(walker.getSnpEffRodBinding()); @@ -225,7 +225,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue())); } - public Map annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc ) { + public Map annotate ( RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc ) { RodBinding snpEffRodBinding = walker.getSnpEffRodBinding(); // Get only SnpEff records that start at this locus, not merely span it: diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index d7529c8ef..af2df8e6a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -22,7 +22,7 @@ import java.util.Map; */ public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index c4d6ea474..eced387b3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -27,10 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; @@ -48,7 +47,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa private static final String STR_PRESENT = "STR"; private static final String REPEAT_UNIT_KEY = "RU"; private static final String REPEATS_PER_ALLELE_KEY = "RPA"; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isIndel()) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java index f4feb9aa8..63694d809 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -28,7 +28,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi private String n454 ="Num454"; private String nSolid = "NumSOLiD"; private String nOther = "NumOther"; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java index 1f8ccf652..2e3578dcb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; @@ -28,7 +28,7 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen private Set trios = null; private final static int MIN_NUM_VALID_TRIOS = 5; // don't calculate this population-level statistic if there are less than X trios with full genotype likelihood information - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( trios == null ) { if ( walker instanceof VariantAnnotator ) { trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents(); 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 8f7f46c20..d6d2beb91 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -38,8 +38,8 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -79,7 +79,7 @@ import java.util.*; @Allows(value={DataSource.READS, DataSource.REFERENCE}) @Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) -public class VariantAnnotator extends RodWalker implements AnnotatorCompatibleWalker { +public class VariantAnnotator extends RodWalker implements AnnotatorCompatible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 46212c19c..073faf54e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -46,7 +46,7 @@ public class VariantAnnotatorEngine { private List requestedExpressions = new ArrayList(); private final HashMap, String> dbAnnotations = new HashMap, String>(); - private final AnnotatorCompatibleWalker walker; + private final AnnotatorCompatible walker; private final GenomeAnalysisEngine toolkit; private boolean requireStrictAlleleMatch = false; @@ -75,7 +75,7 @@ public class VariantAnnotatorEngine { } // use this constructor if you want all possible annotations - public VariantAnnotatorEngine(List annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) { + public VariantAnnotatorEngine(List annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) { this.walker = walker; this.toolkit = toolkit; requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations(); @@ -85,7 +85,7 @@ public class VariantAnnotatorEngine { } // use this constructor if you want to select specific annotations (and/or interfaces) - public VariantAnnotatorEngine(List annotationGroupsToUse, List annotationsToUse, List annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) { + public VariantAnnotatorEngine(List annotationGroupsToUse, List annotationsToUse, List annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) { this.walker = walker; this.toolkit = toolkit; initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java index 1331ad5df..f610a2ba8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; -public interface AnnotatorCompatibleWalker { +public interface AnnotatorCompatible { // getter methods for various used bindings public abstract RodBinding getSnpEffRodBinding(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index c44c834de..bc20f6c97 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -9,12 +9,11 @@ import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; -import java.util.Map; public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts/genotype split by sample - public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, + public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index b94bee31b..1569a605f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -11,7 +11,7 @@ import java.util.Map; public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts split by sample - public abstract Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, + public abstract Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc); // return the descriptions used for the VCF INFO meta field 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 521f89016..996d85a67 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 @@ -37,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation { public abstract List getKeyNames(); // initialization method (optional for subclasses, and therefore non-abstract) - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ) { } + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 31006f4d8..627d561f6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -31,13 +31,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -72,7 +72,7 @@ import static java.lang.Math.log10;

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

*/ -public class BeagleOutputToVCFWalker extends RodWalker { +public class BeagleOutputToVCF extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index a8e280f43..14e92a066 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -37,10 +37,13 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.PrintStream; @@ -72,7 +75,7 @@ import java.util.*; * */ -public class ProduceBeagleInputWalker extends RodWalker { +public class ProduceBeagleInput extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index d6b19b377..6d83a1d2a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -38,12 +38,12 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.Arrays; @@ -54,7 +54,7 @@ import java.util.Set; * in input variant file. Will additional hold back a fraction of the sites for evaluation, marking the * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file */ -public class VariantsToBeagleUnphasedWalker extends RodWalker { +public class VariantsToBeagleUnphased extends RodWalker { @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @@ -104,7 +104,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker GenomeLoc loc = context.getLocation(); VariantContext vc = tracker.getFirstValue(variants, loc); - if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) { + if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) { // do we want to hold back this site? boolean makeMissing = dropSite(vc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java index 8210a11b7..1a03ce1ce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java @@ -47,7 +47,7 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.PrintStream; import java.lang.reflect.Constructor; -import java.util.*; +import java.util.ArrayList; /** * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). @@ -106,7 +106,7 @@ import java.util.*; @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta -public class BaseQualityScoreRecalibrator extends LocusWalker implements TreeReducible { +public class BQSR extends LocusWalker implements TreeReducible { @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index 34d99c018..55c04f1b7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP * @return the covariate keysets for this read */ protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) { - return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE); + return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 2a8940de0..bc791a5a4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -120,7 +120,7 @@ import java.io.PrintStream; * @since May 7, 2010 */ @By(DataSource.REFERENCE) -public class CallableLociWalker extends LocusWalker { +public class CallableLoci extends LocusWalker { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java similarity index 74% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index cd5fdc505..64a51f1b3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -41,7 +41,7 @@ import java.util.List; /** * Test routine for new VariantContext object */ -public class CompareCallableLociWalker extends RodWalker, long[][]> { +public class CompareCallableLoci extends RodWalker, long[][]> { @Output protected PrintStream out; @@ -54,8 +54,8 @@ public class CompareCallableLociWalker extends RodWalker map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + public List map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if ( tracker != null ) { - CallableLociWalker.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1); - CallableLociWalker.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2); + CallableLoci.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1); + CallableLoci.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2); if ( printState != null && comp1.getState() == printState1 && comp2.getState() == printState2 ) { out.printf("%s %s %s %s%n", comp1.getLocation(), comp1.getState(), comp2.getLocation(), comp2.getState()); @@ -92,7 +92,7 @@ public class CompareCallableLociWalker extends RodWalker rodBinding) { + private CallableLoci.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding rodBinding) { //System.out.printf("tracker %s%n", tracker); List bindings = tracker.getValues(rodBinding); if ( bindings.size() != 1 ) { @@ -101,8 +101,8 @@ public class CompareCallableLociWalker extends RodWalker comps, long[][] sum) { + public long[][] reduce(List comps, long[][] sum) { if ( comps != null ) { - CallableLociWalker.CallableBaseState comp1 = comps.get(0); - CallableLociWalker.CallableBaseState comp2 = comps.get(1); + CallableLoci.CallableBaseState comp1 = comps.get(0); + CallableLoci.CallableBaseState comp2 = comps.get(1); sum[comp1.getState().ordinal()][comp2.getState().ordinal()]++; } @@ -127,8 +127,8 @@ public class CompareCallableLociWalker extends RodWalker>, CoveragePartitioner> implements TreeReducible { +public class DepthOfCoverage extends LocusWalker>, CoveragePartitioner> implements TreeReducible { @Output @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"}) Map out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java index 124be2eb4..77d3aa897 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java @@ -63,7 +63,7 @@ import java.util.List; @Allows(value = {DataSource.REFERENCE}) @Requires(value = {DataSource.REFERENCE}) @By(DataSource.REFERENCE) -public class GCContentByIntervalWalker extends LocusWalker { +public class GCContentByInterval extends LocusWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index ac60f5f28..8c4cab877 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import java.io.PrintStream; @@ -56,7 +55,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker { } @Override - public GenomeLoc map(final ActiveRegion activeRegion, final RefMetaDataTracker tracker) { + public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) { if (activeRegion.isActive) return activeRegion.getLocation(); else diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java index 2b7a5612b..a04c4f01b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java @@ -131,7 +131,7 @@ import java.util.List; * @author Mark DePristo * @since 7/4/11 */ -public class DiffObjectsWalker extends RodWalker { +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/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 4e2c17bf6..0d390308e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -73,7 +73,7 @@ import java.util.List; @WalkerName("FastaAlternateReferenceMaker") @Reference(window=@Window(start=-1,stop=50)) @Requires(value={DataSource.REFERENCE}) -public class FastaAlternateReferenceWalker extends FastaReferenceWalker { +public class FastaAlternateReference extends FastaReference { /** * Variants from these input files are used by this tool to construct an alternate reference. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java index 7ae5c5c75..f1eb6d028 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java @@ -67,7 +67,7 @@ import java.io.PrintStream; * */ @WalkerName("FastaReferenceMaker") -public class FastaReferenceWalker extends RefWalker, GenomeLoc> { +public class FastaReference extends RefWalker, GenomeLoc> { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java similarity index 87% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java index f5c5f909f..8a1af623e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java @@ -37,10 +37,10 @@ import java.io.PrintStream; /** * Calculates basic statistics about the reference sequence itself */ -public class FastaStatsWalker extends RefWalker { +public class FastaStats extends RefWalker { @Output PrintStream out; - protected class FastaStats { + protected class FastaStatistics { long nBases = 0, nRegBases = 0; } @@ -50,19 +50,19 @@ public class FastaStatsWalker extends RefWalker { +public class VariantFiltration extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index d504badab..10c8c0d69 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -35,16 +35,16 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.*; @@ -121,7 +121,7 @@ import java.util.*; // TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources: // TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} ) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250) -public class UnifiedGenotyper extends LocusWalker, UnifiedGenotyper.UGStatistics> implements TreeReducible, AnnotatorCompatibleWalker { +public class UnifiedGenotyper extends LocusWalker, UnifiedGenotyper.UGStatistics> implements TreeReducible, AnnotatorCompatible { @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 504359f3f..ef0909c2f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.JexlEngine; @@ -53,7 +52,6 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature; import org.broadinstitute.sting.utils.codecs.refseq.Transcript; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.collections.CircularArray; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.StingException; @@ -64,6 +62,7 @@ import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.*; import java.util.*; @@ -127,7 +126,7 @@ import java.util.*; */ @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class}) -public class SomaticIndelDetectorWalker extends ReadWalker { +public class SomaticIndelDetector extends ReadWalker { // @Output // PrintStream out; @Output(doc="File to write variants (indels) in VCF format",required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java index 4bf24cf86..630d99ce9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java @@ -113,7 +113,7 @@ class PhasingUtils { Map mergedGtAttribs = new HashMap(); PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2); if (phaseQual.PQ != null) - mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ); + mergedGtAttribs.put(ReadBackedPhasing.PQ_KEY, phaseQual.PQ); Genotype mergedGt = new GenotypeBuilder(gt1.getSampleName(), mergedAllelesForSample).log10PError(mergedGQ).attributes(mergedGtAttribs).phased(phaseQual.isPhased).make(); mergedGenotypes.add(mergedGt); @@ -373,7 +373,7 @@ class PhasingUtils { public PhaseAndQuality(Genotype gt) { this.isPhased = gt.isPhased(); if (this.isPhased) { - this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1); + this.PQ = gt.getAttributeAsDouble(ReadBackedPhasing.PQ_KEY, -1); if ( this.PQ == -1 ) this.PQ = null; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index 261c51bcc..154c8c789 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr // Filter out all reads with zero mapping quality @ReadFilters({MappingQualityZeroFilter.class}) -public class ReadBackedPhasingWalker extends RodWalker { +public class ReadBackedPhasing extends RodWalker { private static final boolean DEBUG = false; /** * The VCF file we are phasing variants from. @@ -255,7 +255,7 @@ public class ReadBackedPhasingWalker extends RodWalker { +public class CountBases extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { return read.getReadLength(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java index 09113704a..11cf0fe39 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java @@ -37,7 +37,7 @@ import java.io.PrintStream; * * */ -public class CountLociWalker extends LocusWalker implements TreeReducible { +public class CountLoci extends LocusWalker implements TreeReducible { @Output(doc="Write count to this file instead of STDOUT") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java index dbbd8e761..0856fcda0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * --read-filter command line argument). Simplest example of a read-backed analysis. */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountMalesWalker extends ReadWalker { +public class CountMales extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { Sample sample = getSampleDB().getSample(read); return sample.getGender() == Gender.MALE ? 1 : 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java index edbd5ff75..67ecea1f0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java @@ -70,7 +70,7 @@ import java.util.*; * * */ -public class CountRODsWalker extends RodWalker, Long>> implements TreeReducible, Long>> { +public class CountRODs extends RodWalker, Long>> implements TreeReducible, Long>> { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java similarity index 90% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java index 7c7d6417a..f71362c40 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java @@ -63,7 +63,7 @@ import java.util.List; * * */ -public class CountRODsByRefWalker extends RefWalker, Long>> { +public class CountRODsByRef extends RefWalker, Long>> { /** * One or more input rod files @@ -77,14 +77,14 @@ public class CountRODsByRefWalker extends RefWalker, Long> reduce(CountRODsWalker.Datum point, Pair, Long> sum) { + public Pair, Long> reduce(CountRODs.Datum point, Pair, Long> sum) { return crw.reduce(point, sum); } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index c5ab0426d..d0c917650 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -42,7 +42,7 @@ import java.util.Map; @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountReadEventsWalker extends ReadWalker> , Map>> { +public class CountReadEvents extends ReadWalker> , Map>> { @Output (doc = "GATKReport table output") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index b5a2d183f..c9108054e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountReadsWalker extends ReadWalker { +public class CountReads extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { return 1; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index 9208cbae8..1fff50800 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -37,7 +37,7 @@ import java.util.List; * */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountTerminusEventWalker extends ReadWalker, Pair> { +public class CountTerminusEvent extends ReadWalker, Pair> { public Pair map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { List cigarElements = read.getCigar().getCigarElements(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java index 1cb1579d0..86d8458de 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java @@ -56,7 +56,7 @@ import java.util.*; * --read-filter command line argument). Simplest example of a read-backed analysis. */ @Requires({DataSource.READS}) -public class CycleQualityWalker extends ReadWalker { +public class CycleQuality extends ReadWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java index 6f0490fd3..500f27980 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java @@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException; /** * a walker that simply throws errors. Allows us to test that the engine is behaving as expected with error handling */ -public class ErrorThrowingWalker extends RodWalker implements TreeReducible { +public class ErrorThrowing extends RodWalker implements TreeReducible { @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/QCRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java similarity index 90% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index ab5324e39..814f1c8c2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -26,24 +26,15 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.SAMSequenceRecord; -import org.broad.tribble.Feature; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.StingException; import java.io.PrintStream; -import java.util.Collections; -import java.util.List; /** * Prints out counts of the number of reference ordered data objects encountered. @@ -67,7 +58,7 @@ import java.util.List; * * */ -public class QCRefWalker extends RefWalker { +public class QCRef extends RefWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index 27f9d7b6d..92030a7d9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -52,7 +52,7 @@ import java.util.Arrays; * of the clipping to the output stream. */ @Requires({DataSource.READS}) -public class ReadClippingStatsWalker extends ReadWalker { +public class ReadClippingStats extends ReadWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java index 4425f92c4..5f062c861 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java @@ -44,7 +44,7 @@ import java.util.List; * the same read is not passed to the walker multiple consecutive times. * @author aaron */ -public class ReadValidationWalker extends ReadWalker { +public class ReadValidation extends ReadWalker { // our MD5 sum private MessageDigest m; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java index c9602cd6f..3a9add950 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java @@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; @@ -51,7 +50,7 @@ import java.util.List; * a walker for validating (in the style of validating pile-up) the ROD system. */ @Reference(window=@Window(start=-40,stop=40)) -public class RodSystemValidationWalker extends RodWalker { +public class RodSystemValidation extends RodWalker { // the divider to use in some of the text output private static final String DIVIDER = ","; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java index cd17e4592..f249df475 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java @@ -32,9 +32,12 @@ import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -48,7 +51,7 @@ import java.util.Arrays; * should be specified using the command-line argument '-B pileup,SAMPileup,'. */ @Requires(value={DataSource.READS,DataSource.REFERENCE}) -public class ValidatingPileupWalker extends LocusWalker implements TreeReducible { +public class ValidatingPileup extends LocusWalker implements TreeReducible { @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true) RodBinding pileup; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index 2e3fc26f6..3d008de43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -38,10 +38,10 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.Map; import java.util.Set; @@ -195,7 +195,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel; @Reference(window=@Window(start=-200,stop=200)) -public class GenotypeAndValidateWalker extends RodWalker implements TreeReducible { +public class GenotypeAndValidate extends RodWalker implements TreeReducible { /** * The optional output file that will have all the variants used in the Genotype and Validation essay. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 78fe37fa3..cdcac2300 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -30,10 +30,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; @@ -94,7 +96,7 @@ import java.util.*; * * */ -public class ValidationSiteSelectorWalker extends RodWalker { +public class ValidationSiteSelector extends RodWalker { public enum AF_COMPUTATION_MODE { KEEP_AF_SPECTRUM, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index b9e768274..cdf7b19c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; -import com.google.java.contract.Requires; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.util.IntervalTree; import net.sf.samtools.SAMSequenceRecord; @@ -88,7 +87,7 @@ import java.util.*; */ @Reference(window=@Window(start=-50, stop=50)) @PartitionBy(PartitionType.NONE) -public class VariantEvalWalker extends RodWalker implements TreeReducible { +public class VariantEval extends RodWalker implements TreeReducible { public static final String IS_SINGLETON_KEY = "ISSINGLETON"; @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index ff3bf66f7..97a8b4dda 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.MendelianViolation; @@ -104,7 +104,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator { MendelianViolation mv; Map> families; - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { super.initialize(walker); mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false); families = walker.getSampleDB().getFamilies(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index df4c3e860..c08ff379b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -3,23 +3,23 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; public abstract class VariantEvaluator implements Comparable { - private VariantEvalWalker walker; + private VariantEval walker; private final String simpleName; protected VariantEvaluator() { this.simpleName = getClass().getSimpleName(); } - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { this.walker = walker; } - public VariantEvalWalker getWalker() { + public VariantEval getWalker() { return walker; } @@ -57,7 +57,7 @@ public abstract class VariantEvaluator implements Comparable { * @return true if eval was originally a singleton site */ protected static boolean variantWasSingleton(final VariantContext eval) { - return eval.getAttributeAsBoolean(VariantEvalWalker.IS_SINGLETON_KEY, false); + return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false); } public final String getSimpleName() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index 014381bea..71ea6af98 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -29,7 +29,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.GenomeLoc; @@ -150,7 +150,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { } - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { super.initialize(walker); nSamples = walker.getSampleNamesForEvaluation().size(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 07ba424a2..90b6230ca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -13,7 +13,7 @@ import java.util.List; import java.util.Set; public abstract class VariantStratifier implements Comparable, Stratifier { - private VariantEvalWalker variantEvalWalker; + private VariantEval variantEvalWalker; final private String name; final protected ArrayList states = new ArrayList(); @@ -40,7 +40,7 @@ public abstract class VariantStratifier implements Comparable /** * @return a reference to the parent VariantEvalWalker running this stratification */ - public final VariantEvalWalker getVariantEvalWalker() { + public final VariantEval getVariantEvalWalker() { return variantEvalWalker; } @@ -48,7 +48,7 @@ public abstract class VariantStratifier implements Comparable * Should only be called by VariantEvalWalker itself * @param variantEvalWalker */ - public final void setVariantEvalWalker(VariantEvalWalker variantEvalWalker) { + public final void setVariantEvalWalker(VariantEval variantEvalWalker) { this.variantEvalWalker = variantEvalWalker; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java index 390682837..c98c05a9a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java @@ -3,27 +3,27 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.ArrayList; +import java.util.Set; +import java.util.TreeSet; public final class EvaluationContext { // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function - final VariantEvalWalker walker; + final VariantEval walker; private final ArrayList evaluationInstances; private final Set> evaluationClasses; - public EvaluationContext(final VariantEvalWalker walker, final Set> evaluationClasses) { + public EvaluationContext(final VariantEval walker, final Set> evaluationClasses) { this(walker, evaluationClasses, true); } - private EvaluationContext(final VariantEvalWalker walker, final Set> evaluationClasses, final boolean doInitialize) { + private EvaluationContext(final VariantEval walker, final Set> evaluationClasses, final boolean doInitialize) { this.walker = walker; this.evaluationClasses = evaluationClasses; this.evaluationInstances = new ArrayList(evaluationClasses.size()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 3b28747fb..3dcc1f85f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -28,7 +28,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification; @@ -45,10 +45,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; public class VariantEvalUtils { - private final VariantEvalWalker variantEvalWalker; + private final VariantEval variantEvalWalker; Logger logger; - public VariantEvalUtils(VariantEvalWalker variantEvalWalker) { + public VariantEvalUtils(VariantEval variantEvalWalker) { this.variantEvalWalker = variantEvalWalker; this.logger = variantEvalWalker.getLogger(); } @@ -216,7 +216,7 @@ public class VariantEvalUtils { VariantContextBuilder builder = new VariantContextBuilder(vcsub); if ( isSingleton ) - builder.attribute(VariantEvalWalker.IS_SINGLETON_KEY, true); + builder.attribute(VariantEval.IS_SINGLETON_KEY, true); if ( ! hasChrCountAnnotations ) VariantContextUtils.calculateChromosomeCounts(builder, true); @@ -270,7 +270,7 @@ public class VariantEvalUtils { } if ((byFilter || !vcsub.isFiltered())) { - addMapping(mapping, VariantEvalWalker.getAllSampleName(), vcsub); + addMapping(mapping, VariantEval.getAllSampleName(), vcsub); } // Now, if stratifying, split the subsetted vc per sample and add each as a new context diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java index cd645943b..b4e07716c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * Copyright (c) 2012, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,11 +25,17 @@ package org.broadinstitute.sting.utils.help; public class GATKDocUtils { - /** The URL root for RELEASED GATKDOC units */ + /** + * The URL root for RELEASED GATKDOC units + */ public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; - /** The URL root for STABLE GATKDOC units */ + /** + * The URL root for STABLE GATKDOC units + */ public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; - /** The URL root for UNSTABLE GATKDOC units */ + /** + * The URL root for UNSTABLE GATKDOC units + */ public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; /** @@ -49,6 +55,7 @@ public class GATKDocUtils { /** * Returns a full URL http://etc/ linking to the documentation for class (assuming it * exists). Currently points to the RELEASE doc path only. + * * @param c * @return */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java index 41c855329..0ff5ddc6a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * Copyright (c) 2012, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,41 +25,63 @@ package org.broadinstitute.sting.utils.help; import com.sun.javadoc.ClassDoc; +import org.broadinstitute.sting.gatk.Category; import java.util.HashMap; +import java.util.List; import java.util.Map; /** * Simple collection of all relevant information about something the GATKDoclet can document - * + *

* Created by IntelliJ IDEA. * User: depristo * Date: 7/24/11 * Time: 7:59 PM */ class GATKDocWorkUnit implements Comparable { - /** The class that's being documented */ + /** + * The class that's being documented + */ final Class clazz; - /** The name of the thing we are documenting */ + /** + * The name of the thing we are documenting + */ final String name; - /** the filename where we will be writing the docs for this class */ + /** + * the filename where we will be writing the docs for this class + */ final String filename; - /** The name of the documentation group (e.g., walkers, read filters) class belongs to */ + /** + * The name of the documentation group (e.g., walkers, read filters) class belongs to + */ final String group; - /** The documentation handler for this class */ + /** + * The categories that this class belongs to + */ + final List categories; + /** + * The documentation handler for this class + */ final DocumentedGATKFeatureHandler handler; - /** The javadoc documentation for clazz */ + /** + * The javadoc documentation for clazz + */ final ClassDoc classDoc; - /** The annotation that lead to this Class being in GATKDoc */ + /** + * The annotation that lead to this Class being in GATKDoc + */ final DocumentedGATKFeatureObject annotation; - /** When was this walker built, and what's the absolute version number */ + /** + * When was this walker built, and what's the absolute version number + */ final String buildTimestamp, absoluteVersion; // set by the handler String summary; Map forTemplate; - public GATKDocWorkUnit(String name, String filename, String group, + public GATKDocWorkUnit(String name, String filename, String group, List categories, DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler, ClassDoc classDoc, Class clazz, String buildTimestamp, String absoluteVersion) { @@ -67,6 +89,7 @@ class GATKDocWorkUnit implements Comparable { this.name = name; this.filename = filename; this.group = group; + this.categories = categories; this.handler = handler; this.classDoc = classDoc; this.clazz = clazz; @@ -76,6 +99,7 @@ class GATKDocWorkUnit implements Comparable { /** * Called by the GATKDoclet to set handler provided context for this work unit + * * @param summary * @param forTemplate */ @@ -86,6 +110,7 @@ class GATKDocWorkUnit implements Comparable { /** * Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit + * * @return */ public Map indexDataMap() { @@ -99,6 +124,7 @@ class GATKDocWorkUnit implements Comparable { /** * Sort in order of the name of this WorkUnit + * * @param other * @return */ 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 7f26f22f5..f40675a43 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * Copyright (c) 2012, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -24,6 +24,7 @@ package org.broadinstitute.sting.utils.help; +import com.google.gson.Gson; import com.sun.javadoc.ClassDoc; import com.sun.javadoc.RootDoc; import freemarker.template.Configuration; @@ -34,41 +35,51 @@ import org.apache.commons.io.FileUtils; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.broad.tribble.FeatureCodec; +import org.broadinstitute.sting.gatk.Categorize; +import org.broadinstitute.sting.gatk.Category; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; +import java.lang.annotation.Annotation; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; import java.util.*; /** * Javadoc Doclet that combines javadoc, GATK ParsingEngine annotations, and FreeMarker * templates to produce html formatted GATKDocs for walkers * and other classes. - * + *

* 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 - * static list of things to document, and are to be documented + * DocumentedGATKFeature annotation or are in the type heirarchy 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 + * set of things to document * 3 -- for each unit, actually generate an html page documenting it - * as well as links to related features via their units. Writing - * of a specific class HTML is accomplished by a generate DocumentationHandler + * as well as links to related features via their units. Writing + * of a specific class HTML is accomplished by a generate DocumentationHandler * 4 -- write out an index of all units, organized by group - * + *

* The documented classes are restricted to only those with @DocumentedGATKFeature * annotation or are in the STATIC_DOCS class. */ public class GATKDoclet { final protected static Logger logger = Logger.getLogger(GATKDoclet.class); - /** Where we find the help FreeMarker templates */ + /** + * Where we find the help FreeMarker templates + */ final protected static File SETTINGS_DIR = new File("settings/helpTemplates"); - /** Where we write the GATKDoc html directory */ + /** + * Where we write the GATKDoc html directory + */ final protected static File DESTINATION_DIR = new File("gatkdocs"); // ---------------------------------------------------------------------- @@ -88,10 +99,14 @@ public class GATKDoclet { private static final List> testOnlyKeepers = Arrays.asList( DocumentationTest.class, CommandLineGATK.class, UserException.class); - /** The javadoc root doc */ + /** + * The javadoc root doc + */ RootDoc rootDoc; - /** The set of all things we are going to document */ + /** + * The set of all things we are going to document + */ Set myWorkUnits; /** @@ -103,6 +118,7 @@ public class GATKDoclet { * codecs). */ final static Collection STATIC_DOCS = new ArrayList(); + static { STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class, "Reference ordered data (ROD) codecs", @@ -112,6 +128,7 @@ public class GATKDoclet { /** * Extracts the contents of certain types of javadoc and adds them to an XML file. + * * @param rootDoc The documentation root. * @return Whether the JavaDoc run succeeded. * @throws java.io.IOException if output can't be written. @@ -120,8 +137,8 @@ public class GATKDoclet { logger.setLevel(Level.INFO); // load arguments - for(String[] options: rootDoc.options()) { - if(options[0].equals("-build-timestamp")) + for (String[] options : rootDoc.options()) { + if (options[0].equals("-build-timestamp")) buildTimestamp = options[1]; if (options[0].equals("-absolute-version")) absoluteVersion = options[1]; @@ -139,15 +156,16 @@ public class GATKDoclet { /** * Validate the given options against options supported by this doclet. + * * @param option Option to validate. * @return Number of potential parameters; 0 if not supported. */ public static int optionLength(String option) { - if(option.equals("-build-timestamp") || + if (option.equals("-build-timestamp") || option.equals("-absolute-version") || option.equals("-include-hidden")) { return 2; - } else if ( option.equals("-test") ) + } else if (option.equals("-test")) return 1; else return 0; @@ -155,6 +173,7 @@ public class GATKDoclet { /** * Are we supposed to include @Hidden annotations in our documented output? + * * @return */ public boolean showHiddenFeatures() { @@ -162,7 +181,6 @@ public class GATKDoclet { } /** - * * @param rootDoc */ private void processDocs(RootDoc rootDoc) { @@ -172,7 +190,11 @@ public class GATKDoclet { try { // basic setup DESTINATION_DIR.mkdirs(); - FileUtils.copyFile(new File(SETTINGS_DIR + "/style.css"), new File(DESTINATION_DIR + "/style.css")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.css"), new File(DESTINATION_DIR + "/bootstrap.min.css")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.js"), new File(DESTINATION_DIR + "/bootstrap.min.js")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/jquery.min.js"), new File(DESTINATION_DIR + "/jquery.min.js")); + // print the Version number + FileUtils.writeByteArrayToFile(new File(DESTINATION_DIR + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes()); /* ------------------------------------------------------------------- */ /* You should do this ONLY ONCE in the whole application life-cycle: */ @@ -184,31 +206,109 @@ public class GATKDoclet { cfg.setObjectWrapper(new DefaultObjectWrapper()); myWorkUnits = computeWorkUnits(); - for ( GATKDocWorkUnit workUnit : myWorkUnits ) { - processDocWorkUnit(cfg, workUnit); + + Map>> catNav = getCategories(new ArrayList(myWorkUnits)); + + processCategories(catNav, myWorkUnits); + + for (GATKDocWorkUnit workUnit : myWorkUnits) { + processDocWorkUnit(cfg, workUnit, catNav); } processIndex(cfg, new ArrayList(myWorkUnits)); - } catch ( FileNotFoundException e ) { + } catch (FileNotFoundException e) { throw new RuntimeException(e); - } catch ( IOException e ) { + } catch (IOException e) { throw new RuntimeException(e); } } + private void processCategories(Map>> getCategories, Set classes) throws IOException { + List categories = new LinkedList(); + for (Category cat : getCategories.keySet()) { + Map properties = new HashMap(); + properties.put("Name", cat.getDescription()); + properties.put("UrlSlug", cat.name().toLowerCase().replace('_', '-')); + categories.add(properties); + } + writeJson(DESTINATION_DIR + "/categories.json", categories); + + List posts = new LinkedList(); + for (GATKDocWorkUnit unit : classes) { + Map properties = new HashMap(); + properties.put("Post Title", unit.name + " Documentation"); + properties.put("Categories", unit.categories); + List tags = new ArrayList(); + tags.add(unit.name); + tags.add(unit.group); + properties.put("Tags", tags); + String body = String.format("%s

%s

", + GATKDocUtils.URL_ROOT_FOR_RELEASE_GATKDOCS + unit.filename, unit.name + " Documentation", unit.summary); + properties.put("Body", body); + posts.add(properties); + } + + writeJson(DESTINATION_DIR + "/posts.json", posts); + } + + private void writeJson(String filename, Object source) throws IOException { + Gson gson = new Gson(); + BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(filename))), 1024 * 1024); + + out.write(gson.toJson(source)); + + out.close(); + + } + + public static void postRestJson(String URL, String json) { + try { + URL url = new URL(URL); + HttpURLConnection conn = (HttpURLConnection) url.openConnection(); + conn.setDoOutput(true); + conn.setRequestMethod("POST"); + conn.setRequestProperty("Content-Type", "application/json"); + + OutputStream os = conn.getOutputStream(); + os.write(json.getBytes()); + os.flush(); + + if (conn.getResponseCode() != HttpURLConnection.HTTP_CREATED) { + throw new RuntimeException("Failed : HTTP error code : " + + conn.getResponseCode()); + } + + BufferedReader br = new BufferedReader(new InputStreamReader( + (conn.getInputStream()))); + + String output; + System.out.println("Output from Server .... \n"); + while ((output = br.readLine()) != null) { + System.out.println(output); + } + + conn.disconnect(); + } catch (MalformedURLException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + } + /** * Returns the set of all GATKDocWorkUnits that we are going to generate docs for. + * * @return */ private Set computeWorkUnits() { TreeSet m = new TreeSet(); - for ( ClassDoc doc : rootDoc.classes() ) { + for (ClassDoc doc : rootDoc.classes()) { //logger.debug("Considering " + doc); Class clazz = getClassForClassDoc(doc); // don't add anything that's not DocumentationTest if we are in test mode - if ( clazz != null && testOnly && ! testOnlyKeepers.contains(clazz) ) + if (clazz != null && testOnly && !testOnlyKeepers.contains(clazz)) continue; //if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance")) @@ -216,11 +316,12 @@ public class GATKDoclet { DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc); DocumentedGATKFeatureHandler handler = createHandler(doc, feature); - if ( handler != null && handler.includeInDocs(doc) ) { + if (handler != null && handler.includeInDocs(doc)) { logger.info("Generating documentation for class " + doc); String filename = handler.getDestinationFilename(doc, clazz); + Category[] categories = getClassAnnotationValue(clazz, Categorize.class, "value"); GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(), - filename, feature.groupName(), + filename, feature.groupName(), (categories == null) ? new ArrayList() : Arrays.asList(categories), feature, handler, doc, clazz, buildTimestamp, absoluteVersion); m.add(unit); @@ -233,13 +334,14 @@ public class GATKDoclet { /** * Create a handler capable of documenting the class doc according to feature. Returns * null if no appropriate handler is found or doc shouldn't be documented at all. + * * @param doc * @param feature * @return */ private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) { - if ( feature != null ) { - if ( feature.enable() ) { + if (feature != null) { + if (feature.enable()) { DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler(); handler.setDoclet(this); return handler; @@ -261,15 +363,15 @@ public class GATKDoclet { private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) { Class docClass = getClassForClassDoc(doc); - if ( docClass == null ) + if (docClass == null) return null; // not annotated so it shouldn't be documented - if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) { + if (docClass.isAnnotationPresent(DocumentedGATKFeature.class)) { DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class); return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs()); } else { - for ( DocumentedGATKFeatureObject staticDocs : STATIC_DOCS ) { - if ( staticDocs.getClassToDoc().isAssignableFrom(docClass) ) { + for (DocumentedGATKFeatureObject staticDocs : STATIC_DOCS) { + if (staticDocs.getClassToDoc().isAssignableFrom(docClass)) { return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs()); } } @@ -279,26 +381,28 @@ public class GATKDoclet { /** * Return the Java class described by the ClassDoc doc + * * @param doc * @return */ private Class getClassForClassDoc(ClassDoc doc) { try { // todo -- what do I need the ? extends Object to pass the compiler? - return (Class)HelpUtils.getClassForDoc(doc); - } catch ( ClassNotFoundException e) { + return (Class) HelpUtils.getClassForDoc(doc); + } catch (ClassNotFoundException e) { //logger.warn("Couldn't find class for ClassDoc " + doc); // we got a classdoc for a class we can't find. Maybe in a library or something return null; - } catch ( NoClassDefFoundError e ) { + } catch (NoClassDefFoundError e) { return null; - } catch ( UnsatisfiedLinkError e) { + } catch (UnsatisfiedLinkError e) { return null; // naughty BWA bindings } } /** * Create the html index listing all of the GATKDocs features + * * @param cfg * @param indexData * @throws IOException @@ -312,7 +416,7 @@ public class GATKDoclet { try { temp.process(groupIndexData(indexData), out); out.flush(); - } catch ( TemplateException e ) { + } catch (TemplateException e) { throw new ReviewedStingException("Failed to create GATK documentation", e); } } @@ -320,6 +424,7 @@ public class GATKDoclet { /** * Helpful function to create the html index. Given all of the already run GATKDocWorkUnits, * create the high-level grouping data listing individual features by group. + * * @param indexData * @return */ @@ -334,9 +439,9 @@ public class GATKDoclet { List> groups = new ArrayList>(); Set seenDocumentationFeatures = new HashSet(); List> data = new ArrayList>(); - for ( GATKDocWorkUnit workUnit : indexData ) { + for (GATKDocWorkUnit workUnit : indexData) { data.add(workUnit.indexDataMap()); - if ( ! seenDocumentationFeatures.contains(workUnit.annotation.groupName()) ) { + if (!seenDocumentationFeatures.contains(workUnit.annotation.groupName())) { groups.add(toMap(workUnit.annotation)); seenDocumentationFeatures.add(workUnit.annotation.groupName()); } @@ -347,16 +452,20 @@ public class GATKDoclet { root.put("timestamp", buildTimestamp); root.put("version", absoluteVersion); + root.put("categories", getCategories(indexData)); + return root; } /** * Trivial helper routine that returns the map of name and summary given the annotation + * * @param annotation * @return */ private static final Map toMap(DocumentedGATKFeatureObject annotation) { Map root = new HashMap(); + root.put("id", annotation.groupName().replaceAll("\\W", "")); root.put("name", annotation.groupName()); root.put("summary", annotation.summary()); return root; @@ -364,18 +473,20 @@ public class GATKDoclet { /** * Helper function that finding the GATKDocWorkUnit associated with class from among all of the work units + * * @param c the class we are looking for * @return the GATKDocWorkUnit whose .clazz.equals(c), or null if none could be found */ public final GATKDocWorkUnit findWorkUnitForClass(Class c) { - for ( final GATKDocWorkUnit unit : this.myWorkUnits ) - if ( unit.clazz.equals(c) ) + for (final GATKDocWorkUnit unit : this.myWorkUnits) + if (unit.clazz.equals(c)) return unit; return null; } /** * Return the ClassDoc associated with clazz + * * @param clazz * @return */ @@ -390,12 +501,12 @@ public class GATKDoclet { * @param unit * @throws IOException */ - private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit) + private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit, Map>> categories) throws IOException { //System.out.printf("Processing documentation for class %s%n", unit.classDoc); unit.handler.processOne(unit); - + unit.forTemplate.put("catNav", categories); // Get or create a template Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc)); @@ -405,8 +516,59 @@ public class GATKDoclet { Writer out = new OutputStreamWriter(new FileOutputStream(outputPath)); temp.process(unit.forTemplate, out); out.flush(); - } catch ( TemplateException e ) { + } catch (TemplateException e) { throw new ReviewedStingException("Failed to create GATK documentation", e); } } -} + + // hack - todo - is there a better way to process annotations? + private Category[] getClassAnnotationValue(Class classType, Class annotationType, String attributeName) { + Category[] value = null; + + Annotation annotation = classType.getAnnotation(annotationType); + if (annotation != null) { + try { + value = (Category[]) annotation.annotationType().getMethod(attributeName).invoke(annotation); + } catch (Exception ex) { + } + } + + return value; + } + + private Map>> getCategories(List classes) { + Map>> output = new TreeMap>>(); + + for (Category cat : Category.values()) { + output.put(cat, new ArrayList>()); + } + + for (GATKDocWorkUnit unit : classes) { + Category[] categories = getClassAnnotationValue(unit.clazz, Categorize.class, "value"); + + if (categories != null) { + for (Category cat : categories) { + unit.handler.processOne(unit); + + Map datum = unit.indexDataMap(); + + output.get(cat).add(datum); + } + } + } + + return output; + } + + private static String getSimpleVersion(String absoluteVersion) { + String[] parts = absoluteVersion.split("-"); + + // by skipping i=0, there is no trailing separator + for (int i = 1; i < 2; i++) { + parts[0] = parts[0].concat("-"); + parts[0] = parts[0].concat(parts[i]); + } + + return parts[0]; + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index 20f9eccd3..71c82053f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * Copyright (c) 2012, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -28,14 +28,11 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import com.sun.javadoc.ClassDoc; import com.sun.javadoc.FieldDoc; -import com.sun.javadoc.RootDoc; import com.sun.javadoc.Tag; import org.apache.log4j.Logger; import org.broad.tribble.Feature; -import org.broad.tribble.bed.FullBEDFeature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.JVMUtils; @@ -43,7 +40,7 @@ import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; -import java.io.*; +import java.io.IOException; import java.lang.reflect.*; import java.util.*; @@ -59,16 +56,18 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ private static final int MAX_DISPLAY_NAME = 30; - /** The Class we are documenting */ + /** + * The Class we are documenting + */ private GATKDocWorkUnit toProcess; @Override public boolean includeInDocs(ClassDoc doc) { try { Class type = HelpUtils.getClassForDoc(doc); - boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class); - return ! hidden && JVMUtils.isConcrete(type); - } catch ( ClassNotFoundException e ) { + boolean hidden = !getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class); + return !hidden && JVMUtils.isConcrete(type); + } catch (ClassNotFoundException e) { return false; } } @@ -90,7 +89,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { addArgumentBindings(root); addRelatedBindings(root); - toProcess.setHandlerContent((String)root.get("summary"), root); + toProcess.setHandlerContent((String) root.get("summary"), root); } /** @@ -104,34 +103,37 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // Extract overrides from the doc tags. StringBuilder summaryBuilder = new StringBuilder(); - for(Tag tag: toProcess.classDoc.firstSentenceTags()) + for (Tag tag : toProcess.classDoc.firstSentenceTags()) summaryBuilder.append(tag.text()); root.put("summary", summaryBuilder.toString()); root.put("description", toProcess.classDoc.commentText().substring(summaryBuilder.toString().length())); root.put("timestamp", toProcess.buildTimestamp); root.put("version", toProcess.absoluteVersion); + root.put("categories", toProcess.categories); - for(Tag tag: toProcess.classDoc.tags()) { + for (Tag tag : toProcess.classDoc.tags()) { root.put(tag.name(), tag.text()); } } /** * Add bindings describing related GATK capabilites to toProcess + * * @param root */ protected void addRelatedBindings(Map root) { List> extraDocsData = new ArrayList>(); // add in all of the explicitly related items - for ( final Class extraDocClass : toProcess.annotation.extraDocs() ) { + for (final Class extraDocClass : toProcess.annotation.extraDocs()) { final GATKDocWorkUnit otherUnit = getDoclet().findWorkUnitForClass(extraDocClass); - if ( otherUnit == null ) + if (otherUnit == null) throw new ReviewedStingException("Requested extraDocs for class without any documentation: " + extraDocClass); extraDocsData.add( - new HashMap(){{ + new HashMap() {{ put("filename", otherUnit.filename); - put("name", otherUnit.name);}}); + put("name", otherUnit.name); + }}); } root.put("extradocs", extraDocsData); @@ -149,16 +151,16 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("arguments", args); try { // loop over all of the arguments according to the parsing engine - for ( final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc)) ) { + for (final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc))) { // todo -- why can you have multiple ones? ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0); FieldDoc fieldDoc = getFieldDoc(toProcess.classDoc, argumentSource.field.getName()); Map argBindings = docForArgument(fieldDoc, argumentSource, argDef); - if ( ! argumentSource.isHidden() || getDoclet().showHiddenFeatures() ) { + if (!argumentSource.isHidden() || getDoclet().showHiddenFeatures()) { final String kind = docKindOfArg(argumentSource); final Object value = argumentValue(toProcess.clazz, argumentSource); - if ( value != null ) + if (value != null) argBindings.put("defaultValue", prettyPrintValueString(value)); args.get(kind).add(argBindings); @@ -167,31 +169,33 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { } // sort the arguments - for (Map.Entry>> entry : args.entrySet()) { + for (Map.Entry>> entry : args.entrySet()) { entry.setValue(sortArguments(entry.getValue())); } - } catch ( ClassNotFoundException e ) { + } catch (ClassNotFoundException e) { throw new RuntimeException(e); } } /** * Return the argument kind (required, advanced, hidden, etc) of this argumentSource + * * @param argumentSource * @return */ @Requires("argumentSource != null") @Ensures("result != null") private String docKindOfArg(ArgumentSource argumentSource) { - if ( argumentSource.isRequired() ) return "required"; - else if ( argumentSource.isAdvanced() ) return "advanced"; - else if ( argumentSource.isHidden() ) return "hidden"; - else if ( argumentSource.isDeprecated() ) return "depreciated"; + if (argumentSource.isRequired()) return "required"; + else if (argumentSource.isAdvanced()) return "advanced"; + else if (argumentSource.isHidden()) return "hidden"; + else if (argumentSource.isDeprecated()) return "depreciated"; else return "optional"; } /** * Attempts to determine the value of argumentSource in an instantiated version of c + * * @param c * @param argumentSource * @return value of argumentSource, or null if this isn't possible @@ -201,12 +205,12 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // get the value of the field // attempt to instantiate the class final Object instance = makeInstanceIfPossible(toProcess.clazz); - if ( instance != null ) { + if (instance != null) { final Object value = getFieldValue(instance, argumentSource.field.getName()); - if ( value != null ) + if (value != null) return value; - if ( argumentSource.createsTypeDefault() ) { + if (argumentSource.createsTypeDefault()) { try { // handle the case where there's an implicit default return argumentSource.typeDefaultDocString(); } catch (ReviewedStingException e) { @@ -220,6 +224,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Create the argument map for holding class arguments + * * @return */ private Map>> createArgumentMap() { @@ -236,6 +241,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Sorts the individual argument list in unsorted according to CompareArgumentsByName + * * @param unsorted * @return */ @@ -254,9 +260,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { private String elt(Map m) { String v = m.get("name").toString().toLowerCase(); - if ( v.startsWith("--") ) + if (v.startsWith("--")) return v.substring(2); - else if ( v.startsWith("-") ) + else if (v.startsWith("-")) return v.substring(1); else throw new RuntimeException("Expect to see arguments beginning with at least one -, but found " + v); @@ -267,7 +273,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in * instance of class c. * - * @param instance the object to query for the field value + * @param instance the object to query for the field value * @param fieldName the name of the field we are looking for in instance * @return The value assigned to field in the ArgumentCollection, otherwise null */ @@ -280,14 +286,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // @ArgumentCollection // protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); // - for ( Field field : JVMUtils.getAllFields(instance.getClass()) ) { - if ( field.isAnnotationPresent(ArgumentCollection.class) ) { + for (Field field : JVMUtils.getAllFields(instance.getClass())) { + if (field.isAnnotationPresent(ArgumentCollection.class)) { //System.out.printf("Searching for %s in argument collection field %s%n", fieldName, field); Object fieldValue = JVMUtils.getFieldValue(field, instance); Object value = getFieldValue(fieldValue, fieldName); - if ( value != null ) + if (value != null) return value; - } else if ( field.getName().equals(fieldName) ) { + } else if (field.getName().equals(fieldName)) { return JVMUtils.getFieldValue(field, instance); } } @@ -297,38 +303,39 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Pretty prints value - * + *

* Assumes value != null + * * @param value * @return */ private Object prettyPrintValueString(Object value) { - if ( value.getClass().isArray() ) { + if (value.getClass().isArray()) { Class type = value.getClass().getComponentType(); - if ( boolean.class.isAssignableFrom(type) ) - return Arrays.toString((boolean[])value); - if ( byte.class.isAssignableFrom(type) ) - return Arrays.toString((byte[])value); - if ( char.class.isAssignableFrom(type) ) - return Arrays.toString((char[])value); - if ( double.class.isAssignableFrom(type) ) - return Arrays.toString((double[])value); - if ( float.class.isAssignableFrom(type) ) - return Arrays.toString((float[])value); - if ( int.class.isAssignableFrom(type) ) - return Arrays.toString((int[])value); - if ( long.class.isAssignableFrom(type) ) - return Arrays.toString((long[])value); - if ( short.class.isAssignableFrom(type) ) - return Arrays.toString((short[])value); - if ( Object.class.isAssignableFrom(type) ) - return Arrays.toString((Object[])value); + if (boolean.class.isAssignableFrom(type)) + return Arrays.toString((boolean[]) value); + if (byte.class.isAssignableFrom(type)) + return Arrays.toString((byte[]) value); + if (char.class.isAssignableFrom(type)) + return Arrays.toString((char[]) value); + if (double.class.isAssignableFrom(type)) + return Arrays.toString((double[]) value); + if (float.class.isAssignableFrom(type)) + return Arrays.toString((float[]) value); + if (int.class.isAssignableFrom(type)) + return Arrays.toString((int[]) value); + if (long.class.isAssignableFrom(type)) + return Arrays.toString((long[]) value); + if (short.class.isAssignableFrom(type)) + return Arrays.toString((short[]) value); + if (Object.class.isAssignableFrom(type)) + return Arrays.toString((Object[]) value); else throw new RuntimeException("Unexpected array type in prettyPrintValue. Value was " + value + " type is " + type); - } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) { + } else if (RodBinding.class.isAssignableFrom(value.getClass())) { // annoying special case to handle the UnBound() constructor return "none"; - } else if ( value instanceof String ) { + } else if (value instanceof String) { return value.equals("") ? "\"\"" : value; } else { return value.toString(); @@ -337,6 +344,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Attempt to instantiate class c, if possible. Returns null if this proves impossible. + * * @param c * @return */ @@ -344,21 +352,22 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { Object instance = null; try { // don't try to make something where we will obviously fail - if (! c.isEnum() && ! c.isAnnotation() && ! c.isAnonymousClass() && - ! c.isArray() && ! c.isPrimitive() & JVMUtils.isConcrete(c) ) { + if (!c.isEnum() && !c.isAnnotation() && !c.isAnonymousClass() && + !c.isArray() && !c.isPrimitive() & JVMUtils.isConcrete(c)) { instance = c.newInstance(); //System.out.printf("Created object of class %s => %s%n", c, instance); return instance; } else return null; + } catch (IllegalAccessException e) { + } catch (InstantiationException e) { + } catch (ExceptionInInitializerError e) { + } catch (SecurityException e) { } - catch (IllegalAccessException e ) { } - catch (InstantiationException e ) { } - catch (ExceptionInInitializerError e ) { } - catch (SecurityException e ) { } // this last one is super dangerous, but some of these methods catch ClassNotFoundExceptions // and rethrow then as RuntimeExceptions - catch (RuntimeException e) {} + catch (RuntimeException e) { + } return instance; } @@ -366,6 +375,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Create an instance of the GATK parsing engine, for argument processing with GATKDoclet + * * @return */ private ParsingEngine createStandardGATKParsingEngine() { @@ -392,6 +402,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Recursive helper routine to getFieldDoc() + * * @param classDoc * @param name * @param primary @@ -399,21 +410,21 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ private FieldDoc getFieldDoc(ClassDoc classDoc, String name, boolean primary) { //System.out.printf("Looking for %s in %s%n", name, classDoc.name()); - for ( FieldDoc fieldDoc : classDoc.fields(false) ) { + for (FieldDoc fieldDoc : classDoc.fields(false)) { //System.out.printf("fieldDoc " + fieldDoc + " name " + fieldDoc.name()); - if ( fieldDoc.name().equals(name) ) + if (fieldDoc.name().equals(name)) return fieldDoc; Field field = HelpUtils.getFieldForFieldDoc(fieldDoc); - if ( field == null ) + if (field == null) throw new RuntimeException("Could not find the field corresponding to " + fieldDoc + ", presumably because the field is inaccessible"); - if ( field.isAnnotationPresent(ArgumentCollection.class) ) { + if (field.isAnnotationPresent(ArgumentCollection.class)) { ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName()); - if ( typeDoc == null ) + if (typeDoc == null) throw new ReviewedStingException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc"); else { FieldDoc result = getFieldDoc(typeDoc, name, false); - if ( result != null ) + if (result != null) return result; // else keep searching } @@ -421,11 +432,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { } // if we didn't find it here, wander up to the superclass to find the field - if ( classDoc.superclass() != null ) { + if (classDoc.superclass() != null) { return getFieldDoc(classDoc.superclass(), name, false); } - if ( primary ) + if (primary) throw new RuntimeException("No field found for expected field " + name); else return null; @@ -439,20 +450,20 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * @param s1 the short argument name without -, or null if not provided * @param s2 the long argument name without --, or null if not provided * @return A pair of fully qualified names (with - or --) for the argument. The first - * element is the primary display name while the second (potentially null) is a - * synonymous name. + * element is the primary display name while the second (potentially null) is a + * synonymous name. */ Pair displayNames(String s1, String s2) { s1 = s1 == null ? null : "-" + s1; s2 = s2 == null ? null : "--" + s2; - if ( s1 == null ) return new Pair(s2, null); - if ( s2 == null ) return new Pair(s1, null); + if (s1 == null) return new Pair(s2, null); + if (s2 == null) return new Pair(s1, null); String l = s1.length() > s2.length() ? s1 : s2; String s = s1.length() > s2.length() ? s2 : s1; - if ( l.length() > MAX_DISPLAY_NAME ) + if (l.length() > MAX_DISPLAY_NAME) return new Pair(s, l); else return new Pair(l, s); @@ -460,7 +471,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Returns a human readable string that describes the Type type of a GATK argument. - * + *

* This will include parameterized types, so that Set{T} shows up as Set(T) and not * just Set in the docs. * @@ -469,13 +480,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ protected String argumentTypeString(Type type) { if (type instanceof ParameterizedType) { - ParameterizedType parameterizedType = (ParameterizedType)type; + ParameterizedType parameterizedType = (ParameterizedType) type; List subs = new ArrayList(); - for (Type actualType: parameterizedType.getActualTypeArguments()) + for (Type actualType : parameterizedType.getActualTypeArguments()) subs.add(argumentTypeString(actualType)); - return argumentTypeString(((ParameterizedType)type).getRawType()) + "[" + Utils.join(",", subs) + "]"; + return argumentTypeString(((ParameterizedType) type).getRawType()) + "[" + Utils.join(",", subs) + "]"; } else if (type instanceof GenericArrayType) { - return argumentTypeString(((GenericArrayType)type).getGenericComponentType()) + "[]"; + return argumentTypeString(((GenericArrayType) type).getGenericComponentType()) + "[]"; } else if (type instanceof WildcardType) { throw new RuntimeException("We don't support wildcards in arguments: " + type); } else if (type instanceof Class) { @@ -489,18 +500,19 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * Helper routine that returns the Feature.class required by a RodBinding, * either T for RodBinding{T} or List{RodBinding{T}}. Returns null if * the Type doesn't fit either model. + * * @param type * @return */ protected Class getFeatureTypeIfPossible(Type type) { - if ( type instanceof ParameterizedType) { - ParameterizedType paramType = (ParameterizedType)type; - if ( RodBinding.class.isAssignableFrom((Class)paramType.getRawType()) ) { - return (Class)JVMUtils.getParameterizedTypeClass(type); + if (type instanceof ParameterizedType) { + ParameterizedType paramType = (ParameterizedType) type; + if (RodBinding.class.isAssignableFrom((Class) paramType.getRawType())) { + return (Class) JVMUtils.getParameterizedTypeClass(type); } else { - for ( Type paramtype : paramType.getActualTypeArguments() ) { + for (Type paramtype : paramType.getActualTypeArguments()) { Class x = getFeatureTypeIfPossible(paramtype); - if ( x != null ) + if (x != null) return x; } } @@ -512,6 +524,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * High-level entry point for creating a FreeMarker map describing the GATK argument * source with definition def, with associated javadoc fieldDoc. + * * @param fieldDoc * @param source * @param def @@ -521,9 +534,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { Map root = new HashMap(); Pair names = displayNames(def.shortName, def.fullName); - root.put("name", names.getFirst() ); + root.put("name", names.getFirst()); - if ( names.getSecond() != null ) + if (names.getSecond() != null) root.put("synonyms", names.getSecond()); root.put("required", def.required ? "yes" : "no"); @@ -532,11 +545,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("type", argumentTypeString(source.field.getGenericType())); Class featureClass = getFeatureTypeIfPossible(source.field.getGenericType()); - if ( featureClass != null ) { + if (featureClass != null) { // deal with the allowable types FeatureManager manager = new FeatureManager(); List rodTypes = new ArrayList(); - for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass) ) { + for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass)) { rodTypes.add(String.format("%s", GATKDocUtils.htmlFilenameForClass(descriptor.getCodecClass()), descriptor.getName())); @@ -550,14 +563,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("fulltext", fieldDoc.commentText()); // What are our enum options? - if ( def.validOptions != null ) + if (def.validOptions != null) root.put("options", docForEnumArgument(source.field.getType())); // general attributes List attributes = new ArrayList(); - if ( def.required ) attributes.add("required"); - if ( source.isDeprecated() ) attributes.add("depreciated"); - if ( attributes.size() > 0 ) + if (def.required) attributes.add("required"); + if (source.isDeprecated()) attributes.add("depreciated"); + if (attributes.size() > 0) root.put("attributes", Utils.join(", ", attributes)); return root; @@ -566,21 +579,23 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Helper routine that provides a FreeMarker map for an enumClass, grabbing the * values of the enum and their associated javadoc documentation. + * * @param enumClass * @return */ @Requires("enumClass.isEnum()") private List> docForEnumArgument(Class enumClass) { ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); - if ( doc == null ) // || ! doc.isEnum() ) + if (doc == null) // || ! doc.isEnum() ) throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc); List> bindings = new ArrayList>(); - for (final FieldDoc field : doc.fields(false) ) { + for (final FieldDoc field : doc.fields(false)) { bindings.add( - new HashMap(){{ + new HashMap() {{ put("name", field.name()); - put("summary", field.commentText());}}); + put("summary", field.commentText()); + }}); } return bindings; diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java index 2f8b1e9b5..d8905ad35 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java @@ -28,7 +28,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.ArgumentException; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.walkers.PrintReadsWalker; +import org.broadinstitute.sting.gatk.walkers.PrintReads; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.testng.annotations.Test; @@ -71,7 +71,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest { public void testEmptyIntervalSetHandling() throws Exception { GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); - testEngine.setWalker(new PrintReadsWalker()); + testEngine.setWalker(new PrintReads()); testEngine.setIntervals(new GenomeLocSortedSet(null)); testEngine.validateSuppliedIntervals(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java index 6149a1e51..38be6d2a8 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java @@ -24,13 +24,12 @@ package org.broadinstitute.sting.gatk; -import org.testng.Assert; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker; +import org.broadinstitute.sting.gatk.walkers.qc.CountLoci; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.UserException; - +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -48,7 +47,7 @@ public class WalkerManagerUnitTest { @Test public void testPresentWalker() { Walker countLociWalker = walkerManager.createByName("CountLoci"); - Assert.assertEquals(CountLociWalker.class,countLociWalker.getClass()); + Assert.assertEquals(CountLoci.class,countLociWalker.getClass()); } @Test(expectedExceptions=UserException.class) diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java index 564d1e2a3..66585c872 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java @@ -35,8 +35,8 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker; -import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker; +import org.broadinstitute.sting.gatk.walkers.qc.CountLoci; +import org.broadinstitute.sting.gatk.walkers.qc.CountReads; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -99,7 +99,7 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { private enum WalkerType { COUNT_READS { @Override - Walker create() { return new CountReadsWalker(); } + Walker create() { return new CountReads(); } }, COUNT_BASES_IN_READ { @Override @@ -108,8 +108,8 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { COUNT_LOCI { @Override Walker create() { - CountLociWalker walker = new CountLociWalker(); - JVMUtils.setFieldValue(JVMUtils.findField(CountLociWalker.class,"out"),walker,System.out); + CountLoci walker = new CountLoci(); + JVMUtils.setFieldValue(JVMUtils.findField(CountLoci.class,"out"),walker,System.out); return walker; } }; diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java index 9226f97e2..7845515d8 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java @@ -1,25 +1,22 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; +import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker; import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.gatk.walkers.qc.CountReads; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; - -import static org.testng.Assert.fail; - import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -31,6 +28,8 @@ import java.io.PrintStream; import java.util.ArrayList; import java.util.List; +import static org.testng.Assert.fail; + /** * * User: aaron @@ -106,7 +105,7 @@ public class TraverseReadsUnitTest extends BaseTest { bamList = new ArrayList(); bamList.add(bam); - countReadWalker = new CountReadsWalker(); + countReadWalker = new CountReads(); traversalEngine = new TraverseReads(); traversalEngine.initialize(engine); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java index 0fcaad3bf..1aaa00aee 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java @@ -59,7 +59,7 @@ public class PrintReadsUnitTest extends BaseTest { private ReferenceContext bases = null; //private ReferenceContext ref = new ReferenceContext() - PrintReadsWalker walker; + PrintReads walker; ArtificialSAMFileWriter writer; @BeforeMethod @@ -67,7 +67,7 @@ public class PrintReadsUnitTest extends BaseTest { trav = new ArtificialReadsTraversal(); readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads; - walker = new PrintReadsWalker(); + walker = new PrintReads(); writer = new ArtificialSAMFileWriter(); walker.out = writer; walker.initialize(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java index ca06ca699..f6c12f443 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -49,13 +49,13 @@ import java.util.*; public class VariantEvalWalkerUnitTest extends BaseTest { - VariantEvalWalker VEwalker; + VariantEval VEwalker; VariantContext eval; @BeforeMethod public void init() { - VEwalker = new VariantEvalWalker(); + VEwalker = new VariantEval(); eval = new VariantContextBuilder("x", "chr1", 1, 1, Collections.singleton(Allele.create("A", true))).make(); } diff --git a/public/packages/GATK-Picard.xml b/public/packages/GATK-Picard.xml index 29057d398..251f584f7 100644 --- a/public/packages/GATK-Picard.xml +++ b/public/packages/GATK-Picard.xml @@ -17,12 +17,12 @@ - - - - - - + + + + + + diff --git a/settings/helpTemplates/bootstrap.min.css b/settings/helpTemplates/bootstrap.min.css new file mode 100755 index 000000000..a4b669001 --- /dev/null +++ b/settings/helpTemplates/bootstrap.min.css @@ -0,0 +1,727 @@ +/*! + * Bootstrap v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ +.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} +.clearfix:after{clear:both;} +.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} 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ul{display:inline-block;*display:inline;*zoom:1;margin-left:0;margin-bottom:0;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);} +.pagination li{display:inline;} +.pagination a{float:left;padding:0 14px;line-height:34px;text-decoration:none;border:1px solid #ddd;border-left-width:0;} +.pagination a:hover,.pagination .active a{background-color:#f5f5f5;} +.pagination .active a{color:#999999;cursor:default;} +.pagination .disabled span,.pagination .disabled a,.pagination .disabled a:hover{color:#999999;background-color:transparent;cursor:default;} +.pagination li:first-child a{border-left-width:1px;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} +.pagination li:last-child a{-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;} +.pagination-centered{text-align:center;} +.pagination-right{text-align:right;} +.pager{margin-left:0;margin-bottom:18px;list-style:none;text-align:center;*zoom:1;}.pager:before,.pager:after{display:table;content:"";} +.pager:after{clear:both;} +.pager li{display:inline;} +.pager a{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} +.pager a:hover{text-decoration:none;background-color:#f5f5f5;} +.pager .next a{float:right;} +.pager .previous a{float:left;} +.pager .disabled a,.pager .disabled a:hover{color:#999999;background-color:#fff;cursor:default;} +.thumbnails{margin-left:-20px;list-style:none;*zoom:1;}.thumbnails:before,.thumbnails:after{display:table;content:"";} +.thumbnails:after{clear:both;} +.row-fluid .thumbnails{margin-left:0;} +.thumbnails>li{float:left;margin-bottom:18px;margin-left:20px;} +.thumbnail{display:block;padding:4px;line-height:1;border:1px solid #ddd;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 1px rgba(0, 0, 0, 0.075);-moz-box-shadow:0 1px 1px rgba(0, 0, 0, 0.075);box-shadow:0 1px 1px rgba(0, 0, 0, 0.075);} +a.thumbnail:hover{border-color:#0088cc;-webkit-box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);-moz-box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);} +.thumbnail>img{display:block;max-width:100%;margin-left:auto;margin-right:auto;} +.thumbnail .caption{padding:9px;} +.alert{padding:8px 35px 8px 14px;margin-bottom:18px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;} +.alert-heading{color:inherit;} +.alert .close{position:relative;top:-2px;right:-21px;line-height:18px;} +.alert-success{background-color:#dff0d8;border-color:#d6e9c6;color:#468847;} +.alert-danger,.alert-error{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;} +.alert-info{background-color:#d9edf7;border-color:#bce8f1;color:#3a87ad;} +.alert-block{padding-top:14px;padding-bottom:14px;} +.alert-block>p,.alert-block>ul{margin-bottom:0;} +.alert-block p+p{margin-top:5px;} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-o-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}.progress{overflow:hidden;height:18px;margin-bottom:18px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-ms-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(top, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.progress .bar{width:0%;height:18px;color:#ffffff;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-ms-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(top, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-ms-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} +.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;} +.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} +.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} +.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);} +.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.hero-unit{padding:60px;margin-bottom:30px;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} +.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit;} +.tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.tooltip.in{opacity:0.8;filter:alpha(opacity=80);} +.tooltip.top{margin-top:-2px;} +.tooltip.right{margin-left:2px;} +.tooltip.bottom{margin-top:2px;} +.tooltip.left{margin-left:-2px;} +.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} +.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} +.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} +.tooltip-inner{max-width:200px;padding:3px 8px;color:#ffffff;text-align:center;text-decoration:none;background-color:#000000;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.tooltip-arrow{position:absolute;width:0;height:0;} +.popover{position:absolute;top:0;left:0;z-index:1010;display:none;padding:5px;}.popover.top{margin-top:-5px;} +.popover.right{margin-left:5px;} +.popover.bottom{margin-top:5px;} +.popover.left{margin-left:-5px;} +.popover.top .arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} +.popover.right .arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} +.popover.bottom .arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} +.popover.left .arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.popover .arrow{position:absolute;width:0;height:0;} +.popover-inner{padding:3px;width:280px;overflow:hidden;background:#000000;background:rgba(0, 0, 0, 0.8);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);} +.popover-title{padding:9px 15px;line-height:1;background-color:#f5f5f5;border-bottom:1px solid #eee;-webkit-border-radius:3px 3px 0 0;-moz-border-radius:3px 3px 0 0;border-radius:3px 3px 0 0;} +.popover-content{padding:14px;background-color:#ffffff;-webkit-border-radius:0 0 3px 3px;-moz-border-radius:0 0 3px 3px;border-radius:0 0 3px 3px;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.popover-content p,.popover-content ul,.popover-content ol{margin-bottom:0;} +.modal-open .dropdown-menu{z-index:2050;} +.modal-open .dropdown.open{*z-index:2050;} +.modal-open .popover{z-index:2060;} +.modal-open .tooltip{z-index:2070;} +.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;} +.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);} +.modal{position:fixed;top:50%;left:50%;z-index:1050;overflow:auto;width:560px;margin:-250px 0 0 -280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-ms-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;} +.modal.fade.in{top:50%;} +.modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;} +.modal-body{overflow-y:auto;max-height:400px;padding:15px;} +.modal-form{margin-bottom:0;} +.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";} +.modal-footer:after{clear:both;} +.modal-footer .btn+.btn{margin-left:5px;margin-bottom:0;} +.modal-footer .btn-group .btn+.btn{margin-left:-1px;} +.dropup,.dropdown{position:relative;} +.dropdown-toggle{*margin-bottom:-3px;} +.dropdown-toggle:active,.open .dropdown-toggle{outline:0;} +.caret{display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);} +.dropdown .caret{margin-top:8px;margin-left:2px;} +.dropdown:hover .caret,.open .caret{opacity:1;filter:alpha(opacity=100);} +.dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:4px 0;margin:1px 0 0;list-style:none;background-color:#ffffff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);*border-right-width:2px;*border-bottom-width:2px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;}.dropdown-menu.pull-right{right:0;left:auto;} +.dropdown-menu .divider{*width:100%;height:1px;margin:8px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} +.dropdown-menu a{display:block;padding:3px 15px;clear:both;font-weight:normal;line-height:18px;color:#333333;white-space:nowrap;} +.dropdown-menu li>a:hover,.dropdown-menu .active>a,.dropdown-menu .active>a:hover{color:#ffffff;text-decoration:none;background-color:#0088cc;} +.open{*z-index:1000;}.open >.dropdown-menu{display:block;} +.pull-right>.dropdown-menu{right:0;left:auto;} +.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000000;content:"\2191";} +.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px;} 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b=this;setTimeout(function(){b.hide()},150)},click:function(a){a.stopPropagation(),a.preventDefault(),this.select()},mouseenter:function(b){this.$menu.find(".active").removeClass("active"),a(b.currentTarget).addClass("active")}},a.fn.typeahead=function(c){return this.each(function(){var d=a(this),e=d.data("typeahead"),f=typeof c=="object"&&c;e||d.data("typeahead",e=new b(this,f)),typeof c=="string"&&e[c]()})},a.fn.typeahead.defaults={source:[],items:8,menu:'
    ',item:'
    • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery) \ No newline at end of file diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html index 1554a1d40..a753b9ded 100644 --- a/settings/helpTemplates/common.html +++ b/settings/helpTemplates/common.html @@ -1,15 +1,147 @@ -<#macro makeHeader title> - - ${title} - - - + -<#macro headerInfo> - +<#-- + This file contains all the theming neccesary to present GATKDocs on the GATK website + Included are the paths to our bootstrap assets as well as helper functions to generate relevant links -<#macro footerInfo> -

    See also Main index | GATK wiki | GATK support forum

    -

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

    - + --> + <#global siteRoot = "http://gsa-stage:8080/" /> + <#global forum = "http://gatk.vanillaforums.com/" /> + + <#macro makeHeader title isIndex> + + + + + + ${title} documentation + + + + + + + + + + + +
    +
    +
    + GATK Documentation +
    +
    +
    +
    + + +
    + <#if isIndex> +
    + +
    +
    + + + + + <#macro footerInfo> +
    +

    See also Documentation index | GATK Site | GATK support forum

    + +

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

    + + + <#macro pageFooter> +
    +
    + + + + + <#macro getCategories map filter> + + + + \ No newline at end of file diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html index 6c9e9f4e8..d092ec5a0 100644 --- a/settings/helpTemplates/generic.index.template.html +++ b/settings/helpTemplates/generic.index.template.html @@ -1,36 +1,50 @@ <#include "common.html"/> <#macro emitGroup group> - -

    ${group.name}

    -

    - ${group.summary} -

    -

    - - - - <#list data as datum> - <#if datum.group == group.name> - - - - - - -
    NameSummary
    ${datum.name}${datum.summary}
    - - -<@makeHeader title="GATK documentation index"/> - -

    GATK documentation index

    - <@headerInfo /> - <#list groups?sort_by("name") as group> +
    +
    +
    +

    + ${group.name}

     +
    +
    +
    +

    ${group.summary} + +

    + <#if group.id == "GATKwalkers"> +

    Categories

    + <@getCategories map=categories filter="GATK walkers" /> + <#else> + + + + + + <#list data as datum> + <#if datum.group == group.name> + + + + + + +
    NameSummary
    ${datum.name}${datum.summary}
    + +
    +
    +
    +
    + + +<@makeHeader title="GATK documentation index" isIndex=true /> +

    GATK documentation index +${version}

    +
    +<#list groups?sort_by("name") as group> <@emitGroup group=group/> - - - <@footerInfo /> - - + +<@footerInfo /> +<@pageFooter /> diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html index 7fc8cd7bd..7d02fa865 100644 --- a/settings/helpTemplates/generic.template.html +++ b/settings/helpTemplates/generic.template.html @@ -1,8 +1,10 @@ <#include "common.html"/> <#macro argumentlist name myargs> - <#if myargs?size != 0> - ${name} + <#if myargs?size != 0> + + ${name} + <#list myargs as arg> ${arg.name} @@ -11,116 +13,145 @@ ${arg.summary} <#-- - ${arg.required} + < + td>${arg.required} --> - - + + <#macro argumentDetails arg> -

    ${arg.name}<#if arg.synonyms??> / ${arg.synonyms} - (<#if arg.attributes??>${arg.attributes} ${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue})

    +

    ${arg.name} + <#if arg.synonyms??> / ${arg.synonyms} + + ( + <#if arg.attributes??>${arg.attributes} + ${arg.type} + <#if arg.defaultValue??> with default value ${arg.defaultValue} + ) +

    - ${arg.summary}. ${arg.fulltext} - <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the - following types: ${arg.rodTypes} - <#if arg.options??> -
    - The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values: -

    - <#list arg.options as option> -
    ${option.name}
    -
    ${option.summary}
    - -
    - + ${arg.summary}. ${arg.fulltext} + <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the + following types: ${arg.rodTypes} + + <#if arg.options??> +
    + The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values: +
    + <#list arg.options as option> +
    ${option.name}
    +
    ${option.summary}
    + +
    +

    - - + + <#macro relatedByType name type> <#list relatedDocs as relatedDoc> <#if relatedDoc.relation == type>

    ${name}

      - <#list relatedDocs as relatedDoc> - <#if relatedDoc.relation == type> -
    • ${relatedDoc.name} is a ${relatedDoc.relation}
      • - - + <#list relatedDocs as relatedDoc> + <#if relatedDoc.relation == type> +
    • ${relatedDoc.name} is a ${relatedDoc.relation}
      • + +
    - <#break> + <#break> - -<@makeHeader title="${name} documentation"/> - -

    ${name}

    - <@headerInfo /> -

    ${summary}

    - <#if author??> -

    Author

    - ${author} - -

    Introduction

    - ${description} - - <#-- Create the argument summary --> - <#if arguments.all?size != 0> -
    -

    ${name} specific arguments

    - - - - - - - - - - - <@argumentlist name="Required" myargs=arguments.required/> - <@argumentlist name="Optional" myargs=arguments.optional/> - <@argumentlist name="Advanced" myargs=arguments.advanced/> - <@argumentlist name="Hidden" myargs=arguments.hidden/> - <@argumentlist name="Depreciated" myargs=arguments.depreciated/> - -
    NameTypeDefault valueSummary
    - +<#list categories as cat> + + +<@makeHeader title="${name} documentation" isIndex=false /> +
    + + - <#-- Create references to additional capabilities if appropriate --> - <#if extradocs?size != 0> -
    -

    Additional capabilities

    - The arguments described in the entries below can be supplied to this tool to modify - its behavior. For example, the -L argument directs the GATK engine restricts processing - to specific genomic intervals. This capability is available to all GATK walkers. - - - - <#-- This class is related to other documented classes via sub/super relationships --> - <#if relatedDocs?? && relatedDocs?size != 0> -
    -

    Related capabilities

    - <@relatedByType name="Superclasses" type="superclass"/> - <@relatedByType name="Subclasses" type="subclass"/> - - - <#-- List all of the --> - <#if arguments.all?size != 0> -
    - <#-- Create the argument details --> -

    Argument details

    - <#list arguments.all as arg> - <@argumentDetails arg=arg/> - - - - <@footerInfo /> - - +
    + +
    + +

    ${name}

    + +

    ${summary}

    + <#if author??> +

    Author
    + ${author} +

    + + <#if (categories?size > 0) > +

    Categories

    +
      + <#list categories as cat> +
    • ${cat.getDescription()}
      • + +
    + +

    Introduction

    + ${description} + + <#-- Create the argument summary --> + <#if arguments.all?size != 0> +
    +

    ${name} specific arguments

    + + + + + + + + + + + <@argumentlist name="Required" myargs=arguments.required/> + <@argumentlist name="Optional" myargs=arguments.optional/> + <@argumentlist name="Advanced" myargs=arguments.advanced/> + <@argumentlist name="Hidden" myargs=arguments.hidden/> + <@argumentlist name="Depreciated" myargs=arguments.depreciated/> + +
    NameTypeDefault valueSummary
    + + + <#-- Create references to additional capabilities if appropriate --> + <#if extradocs?size != 0> +
    +

    Additional capabilities

    + The arguments described in the entries below can be supplied to this tool to modify + its behavior. For example, the -L argument directs the GATK engine restricts processing + to specific genomic intervals. This capability is available to all GATK walkers. + + + + <#-- This class is related to other documented classes via sub/super relationships --> + <#if relatedDocs?? && relatedDocs?size != 0> +
    +

    Related capabilities

    + <@relatedByType name="Superclasses" type="superclass"/> + <@relatedByType name="Subclasses" type="subclass"/> + + + <#-- List all of the --> + <#if arguments.all?size != 0> +
    + <#-- Create the argument details --> +

    Argument details

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