From dff5ef562b3e3f761281ee46e0d10970db0b788e Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 12 Feb 2013 12:48:20 -0500 Subject: [PATCH] Reorganized walker categories in GATKDocs (@DocumentedGATKFeature details) -- Sorted out contents of BAM Processing vs. Diagnostics & QC Tools -- Moved two validation-related walkers from Diagnostics & QC to Validation Utilities -- Reworded some category names and descriptions to be more explicit and user-friendly --- .../sting/gatk/walkers/annotator/GCContent.java | 2 +- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- .../gatk/walkers/compression/reducereads/CompareBAM.java | 2 +- .../gatk/walkers/compression/reducereads/ReduceReads.java | 2 +- .../gatk/walkers/diagnostics/targets/DiagnoseTargets.java | 2 +- .../walkers/diagnostics/targets/FindCoveredIntervals.java | 2 +- .../sting/gatk/walkers/indels/IndelRealigner.java | 2 +- .../sting/gatk/walkers/indels/LeftAlignIndels.java | 2 +- .../sting/gatk/walkers/indels/RealignerTargetCreator.java | 2 +- .../broadinstitute/sting/alignment/AlignmentValidation.java | 2 +- .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 2 +- .../sting/gatk/examples/CoverageBySample.java | 2 +- .../org/broadinstitute/sting/gatk/filters/ReadFilter.java | 2 +- .../annotator/interfaces/VariantAnnotatorAnnotation.java | 2 +- .../sting/gatk/walkers/coverage/CallableLoci.java | 2 +- .../sting/gatk/walkers/coverage/CompareCallableLoci.java | 2 +- .../sting/gatk/walkers/coverage/GCContentByInterval.java | 2 +- .../sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java | 2 +- .../sting/gatk/walkers/diagnostics/ReadGroupProperties.java | 2 +- .../gatk/walkers/diagnostics/ReadLengthDistribution.java | 2 +- .../sting/gatk/walkers/diffengine/DiffObjects.java | 2 +- .../gatk/walkers/fasta/FastaAlternateReferenceMaker.java | 2 +- .../sting/gatk/walkers/fasta/FastaReferenceMaker.java | 2 +- .../broadinstitute/sting/gatk/walkers/fasta/FastaStats.java | 2 +- .../broadinstitute/sting/gatk/walkers/qc/CountBases.java | 2 +- .../sting/gatk/walkers/qc/CountIntervals.java | 2 +- .../org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java | 2 +- .../broadinstitute/sting/gatk/walkers/qc/CountMales.java | 2 +- .../org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java | 2 +- .../sting/gatk/walkers/qc/CountRODsByRef.java | 2 +- .../sting/gatk/walkers/qc/CountReadEvents.java | 2 +- .../broadinstitute/sting/gatk/walkers/qc/CountReads.java | 2 +- .../sting/gatk/walkers/qc/CountTerminusEvent.java | 2 +- .../org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java | 2 +- .../org/broadinstitute/sting/gatk/walkers/qc/Pileup.java | 2 +- .../org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java | 2 +- .../src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java | 2 +- .../sting/gatk/walkers/qc/ReadClippingStats.java | 2 +- .../sting/gatk/walkers/qc/ValidatingPileup.java | 2 +- .../sting/gatk/walkers/readutils/ClipReads.java | 2 +- .../sting/gatk/walkers/readutils/PrintReads.java | 2 +- .../sting/gatk/walkers/readutils/SplitSamFile.java | 2 +- .../sting/utils/exceptions/UserException.java | 4 ++-- .../org/broadinstitute/sting/utils/help/GATKDocUtils.java | 6 +++--- .../src/org/broadinstitute/sting/utils/help/GATKDoclet.java | 4 ++-- 45 files changed, 49 insertions(+), 49 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 93bdf8c9d..f2fc5b7ba 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -69,7 +69,7 @@ import java.util.Map; /** * The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation { public Map annotate(final RefMetaDataTracker tracker, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e54af01dd..6a6f6d774 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -127,7 +127,7 @@ import java.util.List; * */ -@DocumentedGATKFeature(groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class}) +@DocumentedGATKFeature(groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class}) @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN) @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class}) @PartitionBy(PartitionType.READ) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java index 3c475576a..cf1ac9d0f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java @@ -87,7 +87,7 @@ import java.util.Map; * @since 10/30/11 */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) public class CompareBAM extends LocusWalker, CompareBAM.TestResults> { @Argument(required = true, shortName = "rr", fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index b94baf931..a463c847d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -102,7 +102,7 @@ import java.util.*; * */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.CONTIG) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class}) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=40) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java index 8edd1ecb9..8f1626bd7 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java @@ -104,7 +104,7 @@ import java.util.*; * @author Mauricio Carneiro, Roger Zurawicki * @since 5/8/12 */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @By(value = DataSource.READS) @PartitionBy(PartitionType.INTERVAL) public class DiagnoseTargets extends LocusWalker { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index ac028d860..fd9ad30ce 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.CONTIG) @ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000) public class FindCoveredIntervals extends ActiveRegionWalker { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 044fb1dcf..928aa57ab 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -133,7 +133,7 @@ import java.util.*; * * @author ebanks */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_OUTPUT) public class IndelRealigner extends ReadWalker { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 6e91b8514..6eb2a633c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -87,7 +87,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * * */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) public class LeftAlignIndels extends ReadWalker { @Output(required=false, doc="Output bam") diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 8a4263f3a..4d8dda34a 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -117,7 +117,7 @@ import java.util.TreeSet; * * @author ebanks */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, BadMateFilter.class, Platform454Filter.class, BadCigarFilter.class}) @Reference(window=@Window(start=-1,stop=50)) @Allows(value={DataSource.READS, DataSource.REFERENCE}) diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index 32126f0e3..e2b5037d0 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -48,7 +48,7 @@ import java.util.Iterator; * @author mhanna * @version 0.1 */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) public class AlignmentValidation extends ReadWalker { /** * The supporting BWT index generated using BWT. diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 63c7ef723..d19245476 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -50,7 +50,7 @@ import java.util.*; * gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here, * the gatk engine should deal with any data related information. */ -@DocumentedGATKFeature(groupName = "GATK Engine") +@DocumentedGATKFeature(groupName = "GATK Engine (parameters available to all tools)") public class CommandLineGATK extends CommandLineExecutable { @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") private String analysisName = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java index bbc53f99d..b44406c81 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java @@ -45,7 +45,7 @@ import java.util.Map; /** * Computes the coverage per sample for every position (use with -L argument!). */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CoverageBySample extends LocusWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index af46c2a42..b2fc8dd6f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; * A SamRecordFilter that also depends on the header. */ @DocumentedGATKFeature( - groupName = "Read filters", + groupName = "Read Filters", summary = "GATK Engine arguments that filter or transfer incoming SAM/BAM data files" ) public abstract class ReadFilter implements SamRecordFilter { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 1415c1d7c..5c8d76904 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 @@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.util.List; import java.util.Set; -@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations") +@DocumentedGATKFeature(enable = true, groupName = "Variant Annotations", summary = "Annotations available to VariantAnnotator and the variant callers (some restrictions apply)") public abstract class VariantAnnotatorAnnotation { // return the INFO keys public abstract List getKeyNames(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 79ff97333..564a046da 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -123,7 +123,7 @@ import java.io.PrintStream; * @author Mark DePristo * @since May 7, 2010 */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @By(DataSource.REFERENCE) public class CallableLoci extends LocusWalker { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index 6f1c9d020..ac84277d8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -46,7 +46,7 @@ import java.util.List; /** * Test routine for new VariantContext object */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CompareCallableLoci extends RodWalker, long[][]> { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java index 84520b24b..257386232 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java @@ -63,7 +63,7 @@ import java.util.List; * * */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Allows(value = {DataSource.REFERENCE}) @Requires(value = {DataSource.REFERENCE}) @By(DataSource.REFERENCE) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 13dc238cd..10b02ac7d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -93,7 +93,7 @@ import java.io.PrintStream; * * @author Kiran Garimella, Mark DePristo */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class ErrorRatePerCycle extends LocusWalker { @Output PrintStream out; @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java index 368e0bb5c..b8bd12e87 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java @@ -97,7 +97,7 @@ import java.util.Map; * * @author Mark DePristo */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class ReadGroupProperties extends ReadWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java index 4965521ce..4bf0a05ca 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java @@ -71,7 +71,7 @@ import java.util.List; * @author Kiran Garimela */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class ReadLengthDistribution extends ReadWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java index b7a1fc1bf..e93732681 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java @@ -134,7 +134,7 @@ import java.util.List; * @author Mark DePristo * @since 7/4/11 */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class DiffObjects extends RodWalker { /** * Writes out a file of the DiffEngine format: diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java index 8a5b3530e..582a8304b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java @@ -81,7 +81,7 @@ import java.util.List; * * */ -@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-1,stop=50)) @Requires(value={DataSource.REFERENCE}) public class FastaAlternateReferenceMaker extends FastaReferenceMaker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java index ed3ebe173..84a2025ec 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java @@ -67,7 +67,7 @@ import java.io.PrintStream; * * */ -@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} ) public class FastaReferenceMaker extends RefWalker, GenomeLoc> { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java index ee2530e8b..0862043bf 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java @@ -39,7 +39,7 @@ import java.io.PrintStream; /** * Calculates basic statistics about the reference sequence itself */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class FastaStats extends RefWalker { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java index 148e699ae..b44620c53 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java @@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountBases extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java index 0423c6f0a..c96eb7b6f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java @@ -48,7 +48,7 @@ import java.util.List; * very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to. * This was its very first use. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CountIntervals extends RefWalker { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java index 093241533..9a3dccd70 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java @@ -65,7 +65,7 @@ import java.io.PrintStream; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CountLoci extends LocusWalker implements TreeReducible, NanoSchedulable { @Output(doc="Write count to this file instead of STDOUT") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java index 1545bff83..3a3f21413 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /** * Walks over the input data set, calculating the number of reads seen from male samples for diagnostic purposes. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountMales extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java index a0f943f7e..4cb60db92 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java @@ -73,7 +73,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CountRODs extends RodWalker, Long>> implements TreeReducible, Long>>, NanoSchedulable { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java index 77490be93..7c392716a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java @@ -65,7 +65,7 @@ import java.util.List; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class CountRODsByRef extends RefWalker, Long>> { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index a614b131f..b07729cf9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -66,7 +66,7 @@ import java.util.Map; * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountReadEvents extends ReadWalker> , Map>> { @Output (doc = "GATKReport table output") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index 4c2a5b9dd..ed5868b31 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountReads extends ReadWalker implements NanoSchedulable { public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index cabc2f467..bd3a9425c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -63,7 +63,7 @@ import java.util.List; * [-L input.intervals] * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountTerminusEvent extends ReadWalker, Pair> { public Pair map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java index d8a307ead..902281eb4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java @@ -72,7 +72,7 @@ import java.text.NumberFormat; * reads with QC failure flag set, number of duplicates, percentage mapped, etc. * @author aaron */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS}) public class FlagStat extends ReadWalker implements NanoSchedulable { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java index c931ab8c2..322ba617c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java @@ -54,7 +54,7 @@ import java.util.List; * Associated command: * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class Pileup extends LocusWalker implements TreeReducible, NanoSchedulable { private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java index dc6dde849..b702f50f9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java @@ -42,7 +42,7 @@ import java.io.PrintStream; * Prints out all of the RODs in the input data set. Data is rendered using the toString() method * of the given ROD. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class PrintRODs extends RodWalker { @Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true) public RodBinding input; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index 84a28b05a..3499c6a99 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -61,7 +61,7 @@ import java.io.PrintStream; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) public class QCRef extends RefWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index f45bf638c..5f521c355 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -56,7 +56,7 @@ import java.util.Arrays; * Walks over the input reads, printing out statistics about the read length, number of clipping events, and length * of the clipping to the output stream. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS}) public class ReadClippingStats extends ReadWalker { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java index a23ff27ff..40209a8d7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java @@ -52,7 +52,7 @@ import java.util.Arrays; * each overlapping read, and quality score) to the reference pileup data generated by samtools. Samtools' pileup data * should be specified using the command-line argument '-pileup:SAMPileup '. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) @Requires(value={DataSource.READS,DataSource.REFERENCE}) public class ValidatingPileup extends LocusWalker implements TreeReducible { @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java index 91059edfd..360b508ee 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java @@ -153,7 +153,7 @@ import java.util.regex.Pattern; * @author Mark DePristo * @since 2010 */ -@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS}) public class ClipReads extends ReadWalker { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java index 1f913edc9..b5a74981c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java @@ -90,7 +90,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @ReadTransformersMode(ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER) @Requires({DataSource.READS, DataSource.REFERENCE}) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java index 73b2bddfc..65bda82da 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java @@ -51,7 +51,7 @@ import java.util.Map; * Divides the input data set into separate BAM files, one for each sample in the input data set. The split * files are named concatenating the sample name to the end of the provided outputRoot command-line argument. */ -@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} ) @WalkerName("SplitSamFile") @Requires({DataSource.READS}) public class SplitSamFile extends ReadWalker> { diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 08d5882b1..715dd3fcd 100644 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -46,8 +46,8 @@ import java.io.File; * Time: 2:24:09 PM */ @DocumentedGATKFeature( - groupName = "User exceptions", - summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." ) + groupName = "User Exceptions", + summary = "Errors caused by incorrect user behavior, such as bad files, bad arguments, etc." ) public class UserException extends ReviewedStingException { /** * The URL where people can get help messages. Printed when an error occurs 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 43f84833f..e8596aa78 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -31,11 +31,11 @@ public class GATKDocUtils { */ public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL; /** - * The URL root for STABLE GATKDOC units + * The URL root for STABLE GATKDOC units //TODO: do sthing with this or remove -- URL goes nowhere */ 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 //TODO: do sthing with this or remove -- URL goes nowhere */ public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; @@ -55,7 +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. + * exists). Currently points to the RELEASE doc path only. //TODO: do sthing with other paths or remove ? * * @param c * @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 fc1fc99d6..e119c7f08 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -117,8 +117,8 @@ public class GATKDoclet { static { STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class, - "Reference ordered data (ROD) codecs", - "Tribble codecs for reading reference ordered data such as VCF or BED files")); + "ROD Codecs", + "Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED")); }