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Adding categories for the remaining uncategorized walkers

This commit is contained in:
Eric Banks 2012-07-30 11:35:08 -04:00
parent 4f741b4cd7
commit 79195b97a3
11 changed files with 34 additions and 1 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
import org.broadinstitute.sting.commandline.Argument;
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.DuplicateReadFilter;
@ -11,6 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.HashMap;
import java.util.Map;
@ -39,6 +41,7 @@ import java.util.Map;
* @since 10/30/11
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
public class CompareBAM extends LocusWalker<Map<CompareBAM.TestName, Boolean>, CompareBAM.TestResults> {
@Argument(required = true, shortName = "rr", fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
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@ -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;
@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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;
@ -80,6 +82,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-HaplotypeResolver.ACTIVE_WINDOW,stop= HaplotypeResolver.ACTIVE_WINDOW))
public class HaplotypeResolver extends RodWalker<Integer, Integer> {

3
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -29,11 +29,13 @@ 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.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.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Iterator;
@ -46,6 +48,7 @@ import java.util.Iterator;
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class AlignmentValidation extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.

3
public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
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@ -34,11 +34,13 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
@ -50,6 +52,7 @@ import java.io.File;
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@WalkerName("Align")
public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="target_reference",shortName="target_ref",doc="The reference to which reads in the source file should be aligned. Alongside this reference should sit index files " +

3
public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java
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@ -30,9 +30,11 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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.ReadWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
@ -48,6 +50,7 @@ import java.util.TreeMap;
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class CountBestAlignments extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.

5
public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
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@ -3,10 +3,12 @@ package org.broadinstitute.sting.gatk.examples;
import net.sf.samtools.SAMReadGroupRecord;
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.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -17,8 +19,9 @@ import java.util.List;
import java.util.Map;
/**
* Computes the coverage per sample.
* Computes the coverage per sample for every position (use with -L argument!).
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class CoverageBySample extends LocusWalker<Integer, Integer> {
@Output
protected PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.examples;
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.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;
@ -46,6 +48,7 @@ import java.io.PrintStream;
*
* @author aaron
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements TreeReducible<Long> {
// the possible diploid genotype strings
private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
import net.sf.picard.util.PeekableIterator;
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;
@ -36,6 +37,7 @@ 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.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
@ -80,6 +82,7 @@ import java.util.*;
* @author Mauricio Carneiro, Roger Zurawicki
* @since 5/8/12
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@By(value = DataSource.READS)
@PartitionBy(PartitionType.INTERVAL)
public class DiagnoseTargets extends LocusWalker<Long, Long> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
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;
@ -33,9 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ActiveRegionExtension(extension = 0, maxRegion = 50000)
public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
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@ -26,17 +26,20 @@
package org.broadinstitute.sting.gatk.walkers.fasta;
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.help.DocumentedGATKFeature;
import java.io.PrintStream;
/**
* Calculates basic statistics about the reference sequence itself
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
@Output PrintStream out;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
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@ -32,6 +32,7 @@ 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;
@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;
import java.util.*;
@ -70,6 +72,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
@Output
public PrintStream out;