From 7eb3f54750fa04f244d77de498b955b034d90944 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 25 Jul 2012 21:40:28 -0400 Subject: [PATCH] Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers. --- .../compression/reducereads/ReduceReads.java | 2 + .../gatk/walkers/FindReadsWithNames.java | 115 ----- .../sting/gatk/walkers/FlagStat.java | 3 + .../sting/gatk/walkers/Pileup.java | 3 + .../sting/gatk/walkers/PrintRODs.java | 3 + .../sting/gatk/walkers/SplitSamFile.java | 3 + .../beagle/VariantsToBeagleUnphased.java | 5 +- .../walkers/coverage/CompareCallableLoci.java | 3 + .../walkers/coverage/GCContentByInterval.java | 3 + .../diagnostics/ErrorRatePerCycle.java | 3 + .../diagnostics/ReadLengthDistribution.java | 5 +- .../gatk/walkers/diffengine/DiffObjects.java | 3 + .../gatk/walkers/indels/LeftAlignIndels.java | 3 + .../sting/gatk/walkers/qc/CountBases.java | 14 +- .../sting/gatk/walkers/qc/CountIntervals.java | 3 + .../sting/gatk/walkers/qc/CountMales.java | 7 +- .../sting/gatk/walkers/qc/CountRODsByRef.java | 3 + .../gatk/walkers/qc/CountReadEvents.java | 11 +- .../gatk/walkers/qc/CountTerminusEvent.java | 5 +- .../sting/gatk/walkers/qc/CycleQuality.java | 434 ------------------ .../sting/gatk/walkers/qc/ErrorThrowing.java | 5 + .../sting/gatk/walkers/qc/QCRef.java | 7 +- .../gatk/walkers/qc/ReadClippingStats.java | 3 + .../sting/gatk/walkers/qc/ReadValidation.java | 125 ----- .../gatk/walkers/qc/RodSystemValidation.java | 8 +- .../gatk/walkers/qc/ValidatingPileup.java | 5 +- .../variantutils/FilterLiftedVariants.java | 3 + .../variantutils/LiftoverVariants.java | 3 + .../variantutils/RandomlySplitVariants.java | 3 + .../walkers/variantutils/SelectHeaders.java | 3 + .../variantutils/VariantsToBinaryPed.java | 3 + 31 files changed, 98 insertions(+), 701 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java 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 189575d6f..d2b9803ef 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 @@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.GenomeLocComparator; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -82,6 +83,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.INTERVAL) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class}) public class ReduceReads extends ReadWalker, ReduceReadsStash> { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java deleted file mode 100644 index f6f091cfc..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java +++ /dev/null @@ -1,115 +0,0 @@ -/* - * Copyright (c) 2010 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.walkers; - -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.text.XReadLines; - -import java.io.File; -import java.io.FileNotFoundException; -import java.util.HashSet; -import java.util.Set; - -/** - * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear - * in the input file. It can dynamically merge the contents of multiple input BAM files, resulting - * in merged output sorted in coordinate order. Can also optionally filter reads based on the --read-filter - * command line argument. - */ -@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) -@Requires({DataSource.READS, DataSource.REFERENCE}) -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; - @Argument(fullName = "readNamesToKeep", shortName = "rn", doc="names to keep", required = true) - File readNamesFile = null; - - Set namesToKeep; - - - /** - * The initialize function. - */ - public void initialize() { - try { - namesToKeep = new HashSet(new XReadLines(readNamesFile).readLines()); - } catch (FileNotFoundException e) { - throw new UserException.CouldNotReadInputFile(readNamesFile, e); - } - } - - /** - * The reads filter function. - * - * @param ref the reference bases that correspond to our read, if a reference was provided - * @param read the read itself, as a SAMRecord - * @return true if the read passes the filter, false if it doesn't - */ - public boolean filter(ReferenceContext ref, GATKSAMRecord read) { - return namesToKeep.contains(read.getReadName()); - } - - /** - * The reads map function. - * - * @param ref the reference bases that correspond to our read, if a reference was provided - * @param read the read itself, as a SAMRecord - * @return the read itself - */ - public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) { - return read; - } - - /** - * reduceInit is called once before any calls to the map function. We use it here to setup the output - * bam file, if it was specified on the command line - * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise - */ - public SAMFileWriter reduceInit() { - return out; - } - - /** - * given a read and a output location, reduce by emitting the read - * @param read the read itself - * @param output the output source - * @return the SAMFileWriter, so that the next reduce can emit to the same source - */ - public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) { - output.addAlignment(read); - return output; - } - -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java index e5f77018c..e881dcab7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java @@ -1,8 +1,10 @@ package org.broadinstitute.sting.gatk.walkers; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.PrintStream; @@ -41,6 +43,7 @@ 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} ) @Requires({DataSource.READS}) public class FlagStat extends ReadWalker { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java index 12b575760..0eb3a628d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java @@ -30,10 +30,12 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -60,6 +62,7 @@ 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} ) public class Pileup extends LocusWalker implements TreeReducible { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java index cfc096ea2..d7ae3050e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java @@ -29,9 +29,11 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; @@ -39,6 +41,7 @@ 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} ) 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/SplitSamFile.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java index e0ee072fe..8553569e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java @@ -31,8 +31,10 @@ import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -45,6 +47,7 @@ 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} ) @WalkerName("SplitSamFile") @Requires({DataSource.READS}) public class SplitSamFile extends ReadWalker> { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index 6d83a1d2a..e183a95d8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -39,6 +40,7 @@ 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.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -51,9 +53,10 @@ import java.util.Set; /** * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample - * in input variant file. Will additional hold back a fraction of the sites for evaluation, marking the + * in input variant file. Will additionally hold back a fraction of the sites for evaluation, marking the * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class VariantsToBeagleUnphased extends RodWalker { @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index 64a51f1b3..420beaeda 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -27,12 +27,14 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; import java.util.Arrays; @@ -41,6 +43,7 @@ import java.util.List; /** * Test routine for new VariantContext object */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis 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 77d3aa897..1fe9c2e81 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -32,6 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; import java.util.List; @@ -60,6 +62,7 @@ import java.util.List; * * */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis 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 a48570fc6..471b23930 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -10,6 +11,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -66,6 +68,7 @@ import java.io.PrintStream; * * @author Kiran Garimella, Mark DePristo */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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/ReadLengthDistribution.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java index 0f5432b80..1dc8a7ec1 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 @@ -2,11 +2,13 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.PrintStream; @@ -44,8 +46,7 @@ import java.util.List; * @author Kiran Garimela */ - - +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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 a04c4f01b..92e2e2dc4 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 @@ -27,10 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.File; import java.io.PrintStream; @@ -131,6 +133,7 @@ import java.util.List; * @author Mark DePristo * @since 7/4/11 */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 7490262f2..6047a15b4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -29,10 +29,12 @@ import net.sf.samtools.Cigar; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -65,6 +67,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * * */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) public class LeftAlignIndels extends ReadWalker { @Output(required=false, doc="Output bam") 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 1ec22b03e..0c323934e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java @@ -1,19 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /** - * Walks over the input data set, calculating the number of reads seen for diagnostic purposes. - * - *

- * Can also count the number of reads matching a given criterion using read filters (see the - * --read-filter command line argument). Simplest example of a read-backed analysis. - * + * Walks over the input data set, calculating the number of bases seen for diagnostic purposes. * *

Input

*

@@ -22,20 +19,21 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * *

Output

*

- * Number of reads seen. + * Number of bases seen. *

* *

Examples

* 
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T CountReads \
+ *   -T CountBases \
  *   -o output.txt \
  *   -I input.bam \
  *   [-L input.intervals]
  *
* */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountBases extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker 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 29b649afe..20b54fa66 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java @@ -5,12 +5,14 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; import java.util.Collections; @@ -21,6 +23,7 @@ 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} ) public class CountIntervals extends RefWalker { @Output 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 0856fcda0..bc178119d 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 @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.samples.Gender; @@ -31,13 +32,13 @@ import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /** - * Walks over the input data set, calculating the number of reads seen for diagnostic purposes. - * Can also count the number of reads matching a given criterion using read filters (see the - * --read-filter command line argument). Simplest example of a read-backed analysis. + * 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} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountMales extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { 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 f71362c40..57ddfb083 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 @@ -29,12 +29,14 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.util.Collections; import java.util.List; @@ -63,6 +65,7 @@ import java.util.List; * * */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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 d0c917650..80845c447 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -2,12 +2,14 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -17,7 +19,7 @@ import java.util.HashMap; import java.util.Map; /** - * Walks over the input data set, counting the number of reads ending in insertions/deletions or soft-clips + * Walks over the input data set, counting the number of read events (from the CIGAR operator) * *

Input

*

@@ -26,21 +28,20 @@ import java.util.Map; * *

Output

*

- * Number of reads ending in each category. - *

+ * Number of reads events for each category * *

Examples

* 
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T ReadEndIndels \
+ *   -T CountReadEvents \
  *   -o output.grp \
  *   -I input.bam \
  *   [-L input.intervals]
  *
*/ - +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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/CountTerminusEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index 1fff50800..971b5bb85 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.DataSource; @@ -9,6 +10,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.List; @@ -30,12 +32,13 @@ import java.util.List; * 
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T ReadEndIndels \
+ *   -T CountTerminusEvent \
  *   -o output.txt \
  *   -I input.bam \
  *   [-L input.intervals]
  *
*/ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountTerminusEvent extends ReadWalker, Pair> { public Pair map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java deleted file mode 100644 index 86d8458de..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java +++ /dev/null @@ -1,434 +0,0 @@ -/* - * Copyright (c) 2010 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.walkers.qc; - -import net.sf.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.utils.collections.PrimitivePair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; - -import java.io.*; -import java.util.*; - -/** - * Created by IntelliJ IDEA. - * User: asivache - * Date: Apr 9, 2010 - * Time: 12:16:41 PM - * To change this template use File | Settings | File Templates. - */ - -/** - * Walks over the input data set, calculating the number of reads seen for diagnostic purposes. - * Can also count the number of reads matching a given criterion using read filters (see the - * --read-filter command line argument). Simplest example of a read-backed analysis. - */ -@Requires({DataSource.READS}) -public class CycleQuality extends ReadWalker { - @Output - protected PrintStream out; - - @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+ - "on mapped reads only, while unmapped reads will be discarded", required=false) - protected boolean MAPPED_ONLY = true; - @Argument(fullName="maxReadLength", shortName="rl", doc="maximum read length", required=false) - protected int MAX_READ_LENGTH = 500; - @Argument(fullName="out_prefix",shortName="p",doc="prefix for output report and statistics files",required=true) - protected String PREFIX = null; -// @Argument(fullName="html",shortName="html",doc="produce html-formatted output (starting with h3-level tags) rather than plain text",required=false) - protected boolean HTML = false; - @Argument(fullName="qualThreshold", shortName="Q",doc="flag as problematic all cycles with av. qualities below the threshold (applies only to the generated report)",required=false) - protected double QTHRESHOLD = 10.0; - @Argument(fullName="useBothQualities",shortName="bothQ",required=false,doc="Generate statistics both for currently set and for "+ - "original base qualities (OQ tag, must be present in the bam); two separate data files will be generated.") - protected boolean ASSESS_BOTH_QUALS = false; - - private Map cyclesByLaneMap = null; - private Map cyclesByLibraryMap = null; - private Map cyclesByLaneMapOrig = null; - private Map cyclesByLibraryMapOrig = null; - - public void initialize() { - if ( PREFIX == null ) throw new ReviewedStingException("Prefix for output file(s) must be specified"); - cyclesByLaneMap = new HashMap(); - cyclesByLibraryMap = new HashMap(); - cyclesByLaneMapOrig = new HashMap(); - cyclesByLibraryMapOrig = new HashMap(); - } - - - public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) { - - if ( AlignmentUtils.isReadUnmapped(read) ) return 0; - - SAMReadGroupRecord rg = read.getReadGroup(); - - if ( rg == null ) throw new UserException.ReadMissingReadGroup(read); - - String lane = read.getReadGroup().getPlatformUnit(); - String library = read.getReadGroup().getLibrary(); - - if ( lane == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no platform unit information"); - if ( library == null ) throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has no library information"); - - int end = 0; - - if ( read.getReadPairedFlag() ) { - - if ( read.getFirstOfPairFlag() ) { - if ( read.getSecondOfPairFlag() ) - throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes"); - end = 1; - } else { - if ( ! read.getSecondOfPairFlag() ) - throw new UserException.MalformedBAM(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes"); - end = 2; - } - } - - CycleStats[] byLane = cyclesByLaneMap.get(lane); - CycleStats[] byLib = cyclesByLibraryMap.get(library); - - //byte [] quals = USE_ORIGINAL_QUALS ? AlignmentUtils.getOriginalQualsInCycleOrder(read) : AlignmentUtils.getQualsInCycleOrder(read); - - byte [] quals = AlignmentUtils.getQualsInCycleOrder(read); - - // if end == 0 (single end lane), we allocate array of length 1, otherwise we need two - // elements in the array in order to be able to collect statistics for each end in the pair independently - if ( byLane == null ) cyclesByLaneMap.put(lane,byLane = new CycleStats[(end==0?1:2)]); - if ( byLib == null ) cyclesByLibraryMap.put(library, byLib =new CycleStats[2]); - - if ( end != 0 ) end--; // we will now use 'end' as index into the array of stats - - if ( byLane[end] == null ) byLane[end] = new CycleStats(MAX_READ_LENGTH); - if ( byLib[end] == null ) byLib[end] =new CycleStats(MAX_READ_LENGTH); - byLane[end].add(quals); - byLib[end].add(quals); - - return 1; //To change body of implemented methods use File | Settings | File Templates. - } - - /** - * Provide an initial value for reduce computations. - * - * @return Initial value of reduce. - */ - public Integer reduceInit() { - return 0; //To change body of implemented methods use File | Settings | File Templates. - } - - /** - * Reduces a single map with the accumulator provided as the ReduceType. - * - * @param value result of the map. - * @param sum accumulator for the reduce. - * @return accumulator with result of the map taken into account. - */ - public Integer reduce(Integer value, Integer sum) { - return sum.intValue()+value.intValue(); //To change body of implemented methods use File | Settings | File Templates. - } - - public void onTraversalDone(Integer result) { - if ( HTML ) { - out.println("

Cycle Quality QC

\n"); - out.println("File(s) analyzed:
"); - for ( String fileName : getToolkit().getArguments().samFiles) out.println(fileName+"
"); - out.println("
"); - } - if ( HTML ) out.println("

"); - out.println("\n"+result+" reads analyzed\n"); - if ( HTML ) out.println("

"); - out.println("by platform unit:"); - if ( HTML ) out.println("
"); - report2(cyclesByLaneMap, new File(PREFIX+".byLane.txt"),true); - out.println(); - if ( HTML ) out.println("

"); - out.println("\nby library:"); - if ( HTML ) out.println("
"); - report2(cyclesByLibraryMap, new File(PREFIX+".byLibrary.txt"),true); - out.println(); - if ( HTML ) out.println("

"); - } - - - - private void report2(Map m, File f,boolean summaryReport) { - long totalReads_1 =0; - long totalReads_2 =0; - long totalReads_unpaired = 0; - SortedSet columns = new TreeSet(); - int maxLength = 0; // maximum read length across all lanes/read ends analyzed - - for( Map.Entry e : m.entrySet() ) { - if ( e.getValue()[0].getMaxReadLength() > maxLength ) maxLength = e.getValue()[0].getMaxReadLength(); - - if ( e.getValue().length == 1 || e.getValue().length == 2 && e.getValue()[1] == null ) { - totalReads_unpaired += e.getValue()[0].getReadCount(); // single end lane - } else { - totalReads_1 += e.getValue()[0].getReadCount(); - totalReads_2 += e.getValue()[1].getReadCount(); - if ( e.getValue()[1].getMaxReadLength() > maxLength ) maxLength = e.getValue()[1].getMaxReadLength(); - } - - columns.add(e.getKey()); - } - - if ( summaryReport ) { - if ( totalReads_1 == 0 && totalReads_2 != 0) { - out.println(" End 1: No reads"); - if ( HTML ) out.println("
"); - } - if ( totalReads_2 == 0 && totalReads_1 != 0 ) { - out.println(" End 2: No reads"); - if ( HTML ) out.println("
"); - } - if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) { - out.println(" No reads found."); - if ( HTML ) out.println("
"); - } - } - - if ( totalReads_1 == 0 && totalReads_2 == 0 && totalReads_unpaired == 0 ) return; - - try { - BufferedWriter w = new BufferedWriter(new FileWriter(f)); - - w.write("cycle"); - - for( String col : columns ) { - CycleStats[] data = m.get(col); - if ( summaryReport ) { - out.print(" "); - out.print(col); - } - - CycleStats end1 = data[0]; - int minL = ( end1 == null ? 0 : end1.getMinReadLength() ); - int maxL = ( end1 == null ? 0 : end1.getMaxReadLength() ); - - if ( data.length == 2 && data[1] != null ) { - if ( summaryReport ) { - out.println(": paired"); - if ( HTML ) out.println("
"); - out.println(" Reads analyzed:"); - if ( HTML ) out.println("
"); - } - CycleStats end2 = data[1]; - - out.print( " End 1: "+ ( end1 == null ? 0 : end1.getReadCount()) ); - if ( minL == maxL ) out.println("; read length = "+minL); - else out.println("; WARNING: variable read length = "+minL+"-"+maxL); - if ( HTML ) out.println("
"); - - out.print( " End 2: "+ ( end2 == null ? 0 : end2.getReadCount()) ); - minL = ( end2 == null ? 0 : end2.getMinReadLength() ); - maxL = ( end2 == null ? 0 : end2.getMaxReadLength() ); - if ( minL == maxL ) out.println("; read length = "+minL); - else out.println("; WARNING: variable read length = "+minL+"-"+maxL); - if ( HTML ) out.println("
"); - } - else { - out.println(": unpaired"); - if ( HTML ) out.println("
"); - out.print( " Reads analyzed: "+ ( end1 == null ? 0 : end1.getReadCount()) ); - if ( minL == maxL ) out.println("; read length = "+minL); - else out.println("; WARNING: variable read length = "+minL+"-"+maxL); - if ( HTML ) out.println("
"); - } - - w.write('\t') ; - w.write(col); - if ( data.length == 1 || data.length == 2 && data[1] == null ) { - w.write(".unpaired"); - w.write('\t'); - w.write(col); - w.write(".unpaired.stddev"); - } else { - w.write(".end1"); - w.write('\t'); - w.write(col); - w.write(".end1.stddev"); - w.write('\t') ; - w.write(col); - w.write(".end2"); - w.write('\t'); - w.write(col); - w.write(".end2.stddev"); - } - } - - w.write('\n'); - - int cycle = 0; - - Map> problems = new HashMap>(); - - while ( cycle < maxLength ) { - w.write(Integer.toString(cycle+1)); - for ( String col : columns ) { - - CycleStats[] data = m.get(col); - CycleStats end1 = data[0]; - w.write('\t'); - if ( end1 == null || cycle >= end1.getMaxReadLength() ) w.write(".\t."); - else { - double aq = end1.getCycleQualAverage(cycle); - w.write(String.format("%.4f\t%.4f",aq,end1.getCycleQualStdDev(cycle))); - recordProblem(aq,cycle, problems,col+".End1"); - } - if ( data.length > 1 && data[1] != null ) { - w.write('\t'); - CycleStats end2 = data[1]; - if ( end2 == null || cycle >= end2.getMaxReadLength() ) w.write(".\t."); - else { - double aq = end2.getCycleQualAverage(cycle); - w.write(String.format("%.4f\t%.4f",aq,end2.getCycleQualStdDev(cycle))); - recordProblem(aq,cycle, problems,col+".End2"); - } - } - } - w.write('\n'); - cycle++; - } - w.close(); - - if ( HTML ) out.println("
"); - - if ( HTML ) out.println("
"); - out.println("\nOUTCOME (threshold at Q="+QTHRESHOLD+"):"); - if ( HTML ) out.println("
"); - for ( String col : columns ) { - List lp = problems.get(col+".End1"); - out.print(" "+col+" End1:"); - if ( lp == null ) { - out.print(" GOOD"); - } else { - for ( PrimitivePair.Int p : lp ) { - out.print(" "+(p.first+1)+"-"); - if ( p.second >= 0 ) out.print((p.second+1)); - else out.print("END"); - } - } - out.println(); - if ( HTML ) out.println("
"); - - lp = problems.get(col+".End2"); - out.print(" "+col+" End2:"); - if ( lp == null ) { - out.print(" GOOD"); - } else { - for ( PrimitivePair.Int p : lp ) { - out.print(" "+(p.first+1)+"-"); - if ( p.second >= 0 ) out.print(p.second); - else out.print("END"); - } - } - out.println(); - if ( HTML ) out.println("
"); - } - - } catch (IOException ioe) { - throw new UserException.CouldNotCreateOutputFile(f, "Failed to write report", ioe); - } - } - - - private void recordProblem(double q, int cycle, Map> problems, String name) { - - PrimitivePair.Int p = null; - List lp = null; - if ( q < QTHRESHOLD ) { // there is a problem - if ( ! problems.containsKey(name) ) { - lp = new ArrayList(); - p = new PrimitivePair.Int(cycle,-1); - lp.add(p); - problems.put(name,lp); - } else { - lp = problems.get(name); - p = lp.get(lp.size()-1); - } - if ( p.second != -1 ) { // if we are not already inside a run of bad qual bases - lp.add(new PrimitivePair.Int(cycle,-1)); // start new run - } - } else { // good base - if ( problems.containsKey(name) ) { // only if we had problem intervals at all, we need to check if the last one needs to be closed - lp = problems.get(name); - p = lp.get(lp.size()-1); - if ( p.second == -1 ) p.second = cycle - 1; - } - } - } - - - static class CycleStats { - private long readCount = 0; - private double[] cycleQualsAv = null; - private double[] cycleQualsSd = null; - private int minL = 1000000000; // read min. length - private int maxL = 0; // read max. length - - public CycleStats(int N) { - readCount = 0; - cycleQualsAv = new double[N]; - cycleQualsSd = new double[N]; - } - - public void add(byte[] quals) { - if ( quals.length > cycleQualsAv.length ) - throw new UserException("A read of length "+quals.length+" encountered, which exceeds specified maximum read length"); - if ( quals.length > maxL ) maxL = quals.length; - if ( quals.length < minL ) minL = quals.length; - readCount++; - for ( int i = 0 ; i < quals.length ; i++ ) { - // NOTE: in the update equaltions below, there is no need to check if readCount == 1 (i.e. - // we are initializing with the very first record) or not. Indeed, the arrays are initialized with - // 0; when the very first value arrives, readCount is 1 and cycleQuals[i] gets set to quals[i] (correct!); - // this will also make the second term in the update equation for Sd (quals[i]-cycleQualsAv[i]) equal - // to 0, so Sd will be initially set to 0. - double oldAvg = cycleQualsAv[i]; // save old mean, will need it for calculation of the variance - cycleQualsAv[i] += ( quals[i] - cycleQualsAv[i] ) / readCount; // update mean - cycleQualsSd[i] += ( quals[i] - oldAvg ) * ( quals[i] - cycleQualsAv[i] ); - } - } - - public long getReadCount() { return readCount; } - public int getMaxReadLength() { return maxL; } - public int getMinReadLength() { return minL; } -// long [] getCycleQualSums() { return cycleQuals; } -// long getCycleQualSum(int i) { return cycleQuals[i]; } - double getCycleQualAverage(int i) { return cycleQualsAv[i]; } - double getCycleQualStdDev(int i) { return Math.sqrt( cycleQualsSd[i]/(readCount-1) ); } - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java index 500f27980..a3df3bc13 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java @@ -24,7 +24,9 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -32,10 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; /** * a walker that simply throws errors. Allows us to test that the engine is behaving as expected with error handling */ +@Hidden +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) 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/QCRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index 814f1c8c2..5082645ad 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 @@ -27,17 +27,19 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequence; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; /** - * Prints out counts of the number of reference ordered data objects encountered. + * Quality control for the reference fasta * * *

Input

@@ -54,10 +56,11 @@ import java.io.PrintStream; * 
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T QCRefWalker
+ *   -T QCRef
  *
* */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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 92030a7d9..16d614afc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -27,6 +27,7 @@ import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.DataSource; @@ -35,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -51,6 +53,7 @@ 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} ) @Requires({DataSource.READS}) public class ReadClippingStats extends ReadWalker { @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java deleted file mode 100644 index 5f062c861..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java +++ /dev/null @@ -1,125 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.qc; - -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; - -import java.security.MessageDigest; -import java.security.NoSuchAlgorithmException; -import java.util.ArrayList; -import java.util.List; - - -/* - * Copyright (c) 2009 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. - */ - -/** - * Checks all reads passed through the system to ensure that - * the same read is not passed to the walker multiple consecutive times. - * @author aaron - */ -public class ReadValidation extends ReadWalker { - - // our MD5 sum - private MessageDigest m; - - // private list of md5sums - private final List list = new ArrayList(); - - /** - * The initialize function. - */ - public void initialize() { - try { - m = MessageDigest.getInstance("MD5"); - } catch (NoSuchAlgorithmException e) { - throw new ReviewedStingException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!"); - } - } - - /** - * The reads filter function. - * - * @param ref the reference bases that correspond to our read, if a reference was provided - * @param read the read itself, as a SAMRecord - * @return true if the read passes the filter, false if it doesn't - */ - public boolean filter(ReferenceContext ref, GATKSAMRecord read) { - return true; - } - - /** - * The reads map function. - * - * @param ref the reference bases that correspond to our read, if a reference was provided - * @param read the read itself, as a SAMRecord - * @return the read itself - */ - public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) { - return read; - } - - /** - * reduceInit is called once before any calls to the map function. We use it here to setup the output - * bam file, if it was specified on the command line - * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise - */ - public SAMRecord reduceInit() { - return null; - } - - /** - * given a read and a output location, reduce by emitting the read - * @param read the read itself - * @param output the output source - * @return the SAMFileWriter, so that the next reduce can emit to the same source - */ - public SAMRecord reduce( SAMRecord read, SAMRecord output ) { - if (output == null) - return read; - if ((read.getReferenceIndex() == output.getReferenceIndex()) && (read.getAlignmentStart() < output.getAlignmentStart())) { - logger.error("saw the read " + read.getReadName() + " duplicated, old alignment = " + output.getAlignmentStart()); - } - else if (read.getReferenceIndex() != output.getReferenceIndex()){ - logger.warn("Switching Chromo"); - } - return read; - } - - - /** - * when we're done traversing, close the reads file - * @param output the SAMFileWriter we've used in the reduce phase - */ - public void onTraversalDone( SAMFileWriter output ) { - if (output != null) { - output.close(); - } - } -} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java index 3a9add950..4e67beffe 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java @@ -24,10 +24,8 @@ package org.broadinstitute.sting.gatk.walkers.qc; -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.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; @@ -37,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.*; @@ -49,6 +48,7 @@ import java.util.List; /** * a walker for validating (in the style of validating pile-up) the ROD system. */ +@Hidden @Reference(window=@Window(start=-40,stop=40)) public class RodSystemValidation extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java index f249df475..7dedd8cf1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java @@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -40,6 +41,7 @@ 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.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import java.io.PrintStream; @@ -48,8 +50,9 @@ import java.util.Arrays; /** * At every locus in the input set, compares the pileup data (reference base, aligned base from * 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 '-B pileup,SAMPileup,'. + * should be specified using the command-line argument '-pileup:SAMPileup '. */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", 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/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 43816b0fa..d223adefb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -34,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -45,6 +47,7 @@ import java.util.Set; /** * Filters a lifted-over VCF file for ref bases that have been changed. */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=0,stop=100)) public class FilterLiftedVariants extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 60d41abd5..0d9a4fc03 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -31,6 +31,7 @@ import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -39,6 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -51,6 +53,7 @@ import java.util.*; /** * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class LiftoverVariants extends RodWalker { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 484f7f052..2ab5136a7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -38,6 +39,7 @@ 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.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; @@ -48,6 +50,7 @@ import java.util.*; /** * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results. */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class RandomlySplitVariants extends RodWalker { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java index 378da05d3..f14f6c2a6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.apache.commons.io.FilenameUtils; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -35,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.text.ListFileUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -98,6 +100,7 @@ import java.util.*; * */ @SuppressWarnings("unused") +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class SelectHeaders extends RodWalker implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 1ffb78124..7e82fc454 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -13,6 +14,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -27,6 +29,7 @@ import java.util.*; * work efficiently on large VCFs (or at least give a progress bar). This * produces a binary ped file in individual major mode. */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class VariantsToBinaryPed extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();