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 d793ae159..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 @@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.filters.*; @@ -46,6 +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; @@ -81,6 +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/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 343e6c96c..f5f707690 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -99,6 +101,7 @@ import java.util.*; * @since 8/22/11 */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.LOCUS) @ActiveRegionExtension(extension=65, maxRegion=275) public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatible { diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index d8674c606..b1ad19e69 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -44,16 +44,15 @@ import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; /** + * All command line parameters accepted by all tools in the GATK. + * * The GATK engine itself. Manages map/reduce data access and runs walkers. * * We run command line GATK programs using this class. It gets the command line args, parses them, and hands the * 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", - summary = "Features and arguments for the GATK engine itself, available to all walkers.", - extraDocs = { UserException.class }) +@DocumentedGATKFeature(groupName = "GATK Engine") public class CommandLineGATK extends CommandLineExecutable { @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") private String analysisName = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 1fe2b840f..70b1be0e1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -17,10 +17,7 @@ import java.util.Collection; import java.util.Iterator; import java.util.LinkedList; import java.util.Queue; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.Future; -import java.util.concurrent.FutureTask; +import java.util.concurrent.*; /** * A microscheduler that schedules shards according to a tree-like structure. @@ -118,6 +115,9 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar queueNextShardTraverse(walker, reduceTree); } + if(hasTraversalErrorOccurred()) + throw getTraversalError(); + threadPool.shutdown(); // Merge any lingering output files. If these files aren't ready, @@ -128,11 +128,12 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar try { result = reduceTree.getResult().get(); notifyTraversalDone(walker,result); - } - catch (ReviewedStingException ex) { + } catch (ReviewedStingException ex) { throw ex; - } - catch (Exception ex) { + } catch ( ExecutionException ex ) { + // the thread died and we are failing to get the result, rethrow it as a runtime exception + throw toRuntimeException(ex.getCause()); + } catch (Exception ex) { throw new ReviewedStingException("Unable to retrieve result", ex); } @@ -353,13 +354,18 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar /** * Allows other threads to notify of an error during traversal. */ - protected synchronized void notifyOfTraversalError(Throwable error) { + protected synchronized RuntimeException notifyOfTraversalError(Throwable error) { + // If the error is already a Runtime, pass it along as is. Otherwise, wrap it. + this.error = toRuntimeException(error); + return this.error; + } + + private final RuntimeException toRuntimeException(final Throwable error) { // If the error is already a Runtime, pass it along as is. Otherwise, wrap it. if (error instanceof RuntimeException) - this.error = (RuntimeException)error; + return (RuntimeException)error; else - this.error = new ReviewedStingException("An error occurred during the traversal.", error); - + return new ReviewedStingException("An error occurred during the traversal. Message=" + error.getMessage(), error); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 5ec52cdb8..aefa9c12d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -81,8 +81,7 @@ public class ShardTraverser implements Callable { return accumulator; } catch(Throwable t) { // Notify that an exception has occurred and rethrow it. - microScheduler.notifyOfTraversalError(t); - throw new RuntimeException(t); + throw microScheduler.notifyOfTraversalError(t); } finally { synchronized(this) { complete = true; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java index 589910fc7..a9b437dfd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java @@ -28,11 +28,10 @@ import net.sf.samtools.SAMRecord; */ /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Dec 9, 2009 - * * Filter out duplicate reads. + * + * @author rpoplin + * @since Dec 9, 2009 */ public class DuplicateReadFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java index 4ec451567..3a5ed7d67 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java @@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.samtools.SAMRecord; /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Jul 19, 2010 + * Filter out reads that fail the vendor quality check. * - * Filter out FailsVendorQualityCheck reads. + * @author rpoplin + * @since Jul 19, 2010 */ public class FailsVendorQualityCheckFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java index 9579aac05..700893fcf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java @@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.samtools.SAMRecord; /** - * Created by IntelliJ IDEA. - * User: chartl - * Date: 5/18/11 - * Time: 4:25 PM - * To change this template use File | Settings | File Templates. + * Filter out reads that are not paired, have their mate unmapped, are duplicates, fail vendor quality check or both mate and read are in the same strand. + * + * @author chartl + * @since 5/18/11 */ public class MateSameStrandFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java index 7bcee033f..25f90f2a2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java @@ -4,11 +4,10 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** - * Created by IntelliJ IDEA. - * User: chartl - * Date: 5/2/11 - * Time: 12:20 PM - * To change this template use File | Settings | File Templates. + * Filter out reads that exceed a given max insert size + * + * @author chartl + * @since 5/2/11 */ public class MaxInsertSizeFilter extends ReadFilter { @Argument(fullName = "maxInsertSize", shortName = "maxInsert", doc="Discard reads with insert size greater than the specified value, defaults to 1000000", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java index 29738e499..02da2cf23 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java @@ -28,11 +28,10 @@ import net.sf.samtools.SAMRecord; */ /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Nov 19, 2009 + * Filter out reads that don't have base an original quality quality score tag (usually added by BQSR) * - * Filter out reads that don't have Original Quality scores inside. + * @author rpoplin + * @since Nov 19, 2009 */ public class NoOriginalQualityScoresFilter extends ReadFilter { public boolean filterOut( final SAMRecord read ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java index 50cd30f71..c26f17f88 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java @@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.samtools.SAMRecord; /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Dec 9, 2009 - * * Filter out duplicate reads. + * + * @author rpoplin + * @since Dec 9, 2009 */ public class NotPrimaryAlignmentFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java index 81044b888..9ac8a5847 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java @@ -8,11 +8,10 @@ import java.util.HashSet; import java.util.Set; /** - * Created by IntelliJ IDEA. - * User: asivache - * Date: Sep 21, 2009 - * Time: 2:54:23 PM - * To change this template use File | Settings | File Templates. + * Filter out reads that have blacklisted platform unit tags. (See code documentation for how to create the blacklist). + * + * @author asivache + * @since Sep 21, 2009 */ public class PlatformUnitFilter extends ReadFilter { // a hack: use static in order to be able to fill it with the data from command line at runtime 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 d8caa3dea..641bddb2d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -28,7 +28,6 @@ public abstract class ReadFilter implements SamRecordFilter { * @return true if the SAMRecords matches the filter, otherwise false * @throws UnsupportedOperationException when paired filter not implemented */ - @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass()); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java index a56af56d1..b0be2c7af 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java @@ -1,17 +1,13 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** - * Created by IntelliJ IDEA. - * User: chartl - * Date: 9/19/11 - * Time: 4:09 PM - * To change this template use File | Settings | File Templates. + * Filter out all reads except those with this read name + * + * @author chartl + * @since 9/19/11 */ public class ReadNameFilter extends ReadFilter { @Argument(fullName = "readName", shortName = "rn", doc="Filter out all reads except those with this read name", required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java index 99d6bc154..7c0880b16 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java @@ -31,6 +31,9 @@ import org.broadinstitute.sting.commandline.Argument; import java.util.Set; +/** + * Filter out all reads except those with this sample + */ public class SampleFilter extends ReadFilter { @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true) private Set SAMPLES_TO_KEEP = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java index 2f93cbcae..0f048b8a0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java @@ -30,11 +30,11 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Nov 27, 2009 - * * Only use reads from the specified read group. + * + * @author rpoplin + * @since Nov 27, 2009 + * */ public class SingleReadGroupFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java index e7ee345d2..5a965db99 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java @@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.samtools.SAMRecord; /** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Dec 9, 2009 + * Filter out unmapped reads. * - * Filter out duplicate reads. + * @author rpoplin + * @since Dec 9, 2009 */ public class UnmappedReadFilter extends ReadFilter { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java index fb265d4e0..beafd0870 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java @@ -33,6 +33,7 @@ import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; 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; @@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.clipping.ClippingOp; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.File; @@ -148,6 +150,7 @@ import java.util.regex.Pattern; * @author Mark DePristo * @since 2010 */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS}) public class ClipReads extends ReadWalker { /** 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/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java index 6e9960f3a..8257794d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java @@ -29,11 +29,13 @@ import net.sf.samtools.SAMFileWriter; 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.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.File; @@ -88,6 +90,7 @@ import java.util.TreeSet; * * */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @Requires({DataSource.READS, DataSource.REFERENCE}) public class PrintReads extends ReadWalker { 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/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index 18c383ed9..6cd2e8aea 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -49,10 +49,7 @@ import java.util.List; @ReadFilters(MalformedReadFilter.class) @PartitionBy(PartitionType.NONE) @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT) -@DocumentedGATKFeature( - groupName = "GATK walkers", - summary = "General tools available for running on the command line as part of the GATK package", - extraDocs = {CommandLineGATK.class}) +@DocumentedGATKFeature(groupName = "Uncategorized", extraDocs = {CommandLineGATK.class}) public abstract class Walker { final protected static Logger logger = Logger.getLogger(Walker.class); private GenomeAnalysisEngine toolkit; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 263320d1b..fba30b3f7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +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; @@ -9,6 +10,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; @@ -20,6 +22,7 @@ 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} ) public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation { public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index d6d2beb91..cce106210 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; 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; @@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -75,6 +77,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Requires(value={}) @Allows(value={DataSource.READS, DataSource.REFERENCE}) @Reference(window=@Window(start=-50,stop=50)) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index c8abbfa5a..9eb0e4dda 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.beagle; 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; @@ -36,6 +37,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -72,6 +74,7 @@ import static java.lang.Math.log10;

Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them

*/ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class BeagleOutputToVCF extends RodWalker { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index 470a1d477..fdc333676 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.beagle; import org.broadinstitute.sting.commandline.*; +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; @@ -42,6 +43,7 @@ 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.StingException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -75,6 +77,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class ProduceBeagleInput extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index f338f0124..a6a6d484e 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/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 4cba67909..b2400a49d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.commandline.ArgumentCollection; +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.filters.MappingQualityUnavailableFilter; @@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -97,13 +99,12 @@ import java.util.ArrayList; * */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN) @By(DataSource.READS) - @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta - public class BaseRecalibrator extends LocusWalker implements TreeReducible { @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index bc791a5a4..58ddd0879 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import org.broadinstitute.sting.commandline.Advanced; 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; @@ -35,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import java.io.File; @@ -119,6 +121,7 @@ import java.io.PrintStream; * @author Mark DePristo * @since May 7, 2010 */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis 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 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/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java index 9fc1ec2f3..c5b043b7a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java @@ -29,6 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -48,6 +49,7 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.File; import java.io.PrintStream; @@ -114,6 +116,7 @@ import java.util.*; // todo -- alter logarithmic scaling to spread out bins more // todo -- allow for user to set linear binning (default is logarithmic) // todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @By(DataSource.REFERENCE) @PartitionBy(PartitionType.NONE) @Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java index 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/ReadGroupProperties.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java index e4e3c271e..9289f86e3 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 @@ -27,12 +27,14 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; 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.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.utils.Median; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.PrintStream; @@ -94,6 +96,7 @@ import java.util.Map; * * @author Mark DePristo */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis 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 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/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 0d390308e..9c9a75fc4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -27,12 +27,14 @@ package org.broadinstitute.sting.gatk.walkers.fasta; 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.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Collections; @@ -70,6 +72,7 @@ import java.util.List; * * */ +@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) @WalkerName("FastaAlternateReferenceMaker") @Reference(window=@Window(start=-1,stop=50)) @Requires(value={DataSource.REFERENCE}) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java index f1eb6d028..a835560d4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta; 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; @@ -34,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; @@ -66,6 +68,7 @@ import java.io.PrintStream; * * */ +@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) @WalkerName("FastaReferenceMaker") public class FastaReference extends RefWalker, GenomeLoc> { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java index 1415239b4..8b3886cfb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.filters; 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; @@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; 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.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -75,6 +77,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50,stop=50)) public class VariantFiltration extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index b3a0b2a5d..cd1815d82 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -41,6 +42,7 @@ import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -114,6 +116,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT) @ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} ) @Reference(window=@Window(start=-200,stop=200)) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index addfc5fab..2153525ab 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil; import net.sf.samtools.util.StringUtil; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; @@ -46,6 +47,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; @@ -109,6 +111,7 @@ import java.util.*; * * @author ebanks */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) public class IndelRealigner extends ReadWalker { 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/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 5f39f4ea8..02e4d414d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.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.filters.*; @@ -37,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -94,6 +96,7 @@ import java.util.TreeSet; * * @author ebanks */ +@DocumentedGATKFeature( groupName = "BAM Processing and Analysis 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/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 0c7e2ec5f..84a65b9b2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -32,6 +32,7 @@ import org.apache.commons.jexl2.JexlEngine; import org.apache.commons.jexl2.MapContext; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; @@ -57,6 +58,7 @@ import org.broadinstitute.sting.utils.collections.CircularArray; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; @@ -126,6 +128,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class}) public class SomaticIndelDetector extends ReadWalker { // @Output diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 4760893ca..3cf1d485e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing; 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; @@ -12,6 +13,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.MathUtils; 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.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.*; @@ -72,6 +74,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class PhaseByTransmission extends RodWalker, HashMap> { @ArgumentCollection diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index 154c8c789..f16deb701 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -27,6 +27,7 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Hidden; 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; @@ -40,6 +41,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; 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.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.*; @@ -91,6 +93,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr // Filter out all reads with zero mapping quality @ReadFilters({MappingQualityZeroFilter.class}) +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class ReadBackedPhasing extends RodWalker { private static final boolean DEBUG = false; /** 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/CountLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java index 11cf0fe39..bd10eab87 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java @@ -1,11 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.qc; 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.LocusWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; @@ -37,6 +39,7 @@ import java.io.PrintStream; * * */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) public class CountLoci extends LocusWalker implements TreeReducible { @Output(doc="Write count to this file instead of STDOUT") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/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/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index c9108054e..5a9e5e7d2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -1,10 +1,12 @@ 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; /** @@ -36,6 +38,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * * */ +@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountReads extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker 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 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/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index 3d008de43..5beeeb3e6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.validation; 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.refdata.RefMetaDataTracker; @@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -188,13 +190,11 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel; * @since ${DATE} */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) @Requires(value={DataSource.READS, DataSource.REFERENCE}) @Allows(value={DataSource.READS, DataSource.REFERENCE}) - @By(DataSource.REFERENCE) @Reference(window=@Window(start=-200,stop=200)) - - public class GenotypeAndValidate extends RodWalker implements TreeReducible { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 3d281ef6c..9676704c2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -8,6 +8,7 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWTFiles; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; 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.refdata.RefMetaDataTracker; @@ -18,6 +19,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; @@ -88,6 +90,7 @@ import java.util.List; * @author chartl * @since July 2011 */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) @Requires(value={DataSource.REFERENCE}) public class ValidationAmplicons extends RodWalker { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index cdcac2300..9e5fd25a9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; 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.refdata.RefMetaDataTracker; @@ -33,6 +34,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -96,6 +98,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) public class ValidationSiteSelector extends RodWalker { public enum AF_COMPUTATION_MODE { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index 1b5474777..0b395bc62 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -7,6 +7,7 @@ import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -26,6 +27,7 @@ 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.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; @@ -86,6 +88,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50, stop=50)) @PartitionBy(PartitionType.NONE) public class VariantEval extends RodWalker implements TreeReducible { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 0dfdd4ba1..744a094c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.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; @@ -38,6 +39,7 @@ 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.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -85,6 +87,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.LOCUS) public class ApplyRecalibration extends RodWalker implements TreeReducible { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 244c5d109..2a424e15b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; 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.refdata.RefMetaDataTracker; @@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.io.Resource; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -109,6 +111,7 @@ import java.util.*; * */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.NONE) public class VariantRecalibrator extends RodWalker, ExpandingArrayList> implements TreeReducible> { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 94fa29173..98a8ac92b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; 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.io.stubs.VariantContextWriterStub; @@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; 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; @@ -96,6 +98,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50,stop=50)) public class CombineVariants extends RodWalker { /** 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/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 3f19e22d9..e0b723659 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -30,6 +30,7 @@ import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; 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; @@ -41,6 +42,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; @@ -76,6 +78,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-200,stop=200)) public class LeftAlignVariants extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 094897edc..63209e98c 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/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index fbffd620a..e4831eaf2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; +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; @@ -41,6 +42,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.MendelianViolation; 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.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; @@ -186,6 +188,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class SelectVariants extends RodWalker implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 995e98931..c92551a73 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.TribbleException; 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; @@ -34,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -66,6 +68,7 @@ import java.util.Set; * * */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=0,stop=100)) public class ValidateVariants extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 3fca2d28a..a301867fc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.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.QualityUtils; 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.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -81,6 +83,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=0,stop=40)) public class VariantValidationAssessor extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 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(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 4806b2ebc..adf30146f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -25,10 +25,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; 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.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -97,6 +99,7 @@ import java.util.*; * @author Mark DePristo * @since 2010 */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) public class VariantsToTable extends RodWalker { /** * Variants from this VCF file are used by this tool as input. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index cf568a62e..78c9c4a1c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import net.sf.samtools.util.CloseableIterator; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -44,6 +45,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; 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.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; @@ -78,6 +80,7 @@ import java.util.*; * * */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-40,stop=40)) public class VariantsToVCF extends RodWalker { diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index 86b7e60ff..af4891856 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -95,6 +95,8 @@ public abstract class BaseTest { public static final String keysDataLocation = validationDataLocation + "keys/"; public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key"; + public static final String exampleFASTA = publicTestDir + "exampleFASTA.fasta"; + /** before the class starts up */ static { // setup a basic log configuration diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java index a997385d6..7e38c00f3 100755 --- a/public/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java @@ -169,7 +169,6 @@ public class WalkerTest extends BaseTest { Class expectedException = null; boolean includeImplicitArgs = true; boolean includeShadowBCF = true; - boolean repairHeader = false; // the default output path for the integration test private File outputFileLocation = null; @@ -211,8 +210,6 @@ public class WalkerTest extends BaseTest { String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile)); if ( includeShadowBCF && GENERATE_SHADOW_BCF ) args = args + " --generateShadowBCF "; - if ( repairHeader ) - args = args + " --repairVCFHeader public/data/vcfHeaderForRepairs.vcf "; } return args; @@ -224,7 +221,6 @@ public class WalkerTest extends BaseTest { * which will ultimately blow up... */ public void disableShadowBCF() { this.includeShadowBCF = false; } - public void repairHeaders() { this.repairHeader = true; } public void setOutputFileLocation(File outputFileLocation) { this.outputFileLocation = outputFileLocation; } @@ -367,10 +363,16 @@ public class WalkerTest extends BaseTest { // it's the type we expected //System.out.println(String.format(" => %s PASSED", name)); } else { - if ( e.getCause() != null ) - e.getCause().printStackTrace(System.out); // must print to stdout to see the message - Assert.fail(String.format("Test %s expected exception %s but instead got %s with error message %s", - name, expectedException, e.getClass(), e.getMessage())); + final String message = String.format("Test %s expected exception %s but instead got %s with error message %s", + name, expectedException, e.getClass(), e.getMessage()); + if ( e.getCause() != null ) { + final ByteArrayOutputStream baos = new ByteArrayOutputStream(); + final PrintStream ps = new PrintStream(baos); + e.getCause().printStackTrace(ps); + BaseTest.log(message); + BaseTest.log(baos.toString()); + } + Assert.fail(message); } } else { // we didn't expect an exception but we got one :-( diff --git a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java index 01af55ca3..5c4db08bd 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java @@ -90,7 +90,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { super(EngineErrorHandlingTestProvider.class); this.expectedException = exceptedException; this.multiThreaded = multiThreaded; - this.iterationsToTest = multiThreaded ? 10 : 1; + this.iterationsToTest = multiThreaded ? 1000 : 1; setName(String.format("Engine error handling: expected %s, is-multithreaded %b", exceptedException, multiThreaded)); } } @@ -110,9 +110,9 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { // Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type // @Test(dataProvider = "EngineErrorHandlingTestProvider") - public void testEngineErrorHandlingTestProvider(EngineErrorHandlingTestProvider cfg) { + public void testEngineErrorHandlingTestProvider(final EngineErrorHandlingTestProvider cfg) { for ( int i = 0; i < cfg.iterationsToTest; i++ ) { - final String root = "-T ErrorThrowing -R " + b37KGReference; + final String root = "-T ErrorThrowing -R " + exampleFASTA; final String args = root + (cfg.multiThreaded ? " -nt 2" : "") + " -E " + cfg.expectedException.getSimpleName(); WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException); executeTest(cfg.toString(), spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java index 724c343e4..6264758ad 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -131,7 +131,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest { @Test public void testGenerateIndexForUnindexedFile() { - File vcfFile = new File(validationDataLocation + "/ROD_validation/always_reindex.vcf"); + File vcfFile = new File(privateTestDir + "always_reindex.vcf"); File vcfFileIndex = Tribble.indexFile(vcfFile); // if we can't write to the directory, don't fault the tester, just pass @@ -141,7 +141,8 @@ public class RMDTrackBuilderUnitTest extends BaseTest { } // clean-up our test, and previous tests that may have written the file vcfFileIndex.deleteOnExit(); - if (vcfFileIndex.exists()) vcfFileIndex.delete(); + if (vcfFileIndex.exists()) + vcfFileIndex.delete(); try { builder.loadIndex(vcfFile, new VCFCodec());