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Merge pull request #28 from broadinstitute/gg_reorganize_gatkdocs_categories_GSATDG-62 

Reorganized walker categories in GATKDocs (@DocumentedGATKFeature details)
This commit is contained in:
depristo 2013-02-12 11:11:45 -08:00
parent 59484dfae4 dff5ef562b
commit 38cea0a7ab
45 changed files with 49 additions and 49 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -69,7 +69,7 @@ import java.util.Map;
/**
* The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -127,7 +127,7 @@ import java.util.List;
* </pre>
*/
@DocumentedGATKFeature(groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class})
@DocumentedGATKFeature(groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class})
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
@PartitionBy(PartitionType.READ)

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
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@ -87,7 +87,7 @@ import java.util.Map;
* @since 10/30/11
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
public class CompareBAM extends LocusWalker<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;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -102,7 +102,7 @@ import java.util.*;
* </pre>
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class})
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=40)

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -104,7 +104,7 @@ import java.util.*;
* @author Mauricio Carneiro, Roger Zurawicki
* @since 5/8/12
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@By(value = DataSource.READS)
@PartitionBy(PartitionType.INTERVAL)
public class DiagnoseTargets extends LocusWalker<Long, Long> {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000)
public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -133,7 +133,7 @@ import java.util.*;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_OUTPUT)
public class IndelRealigner extends ReadWalker<Integer, Integer> {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
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@ -87,7 +87,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
@Output(required=false, doc="Output bam")

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -117,7 +117,7 @@ import java.util.TreeSet;
*
* @author ebanks
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, BadMateFilter.class, Platform454Filter.class, BadCigarFilter.class})
@Reference(window=@Window(start=-1,stop=50))
@Allows(value={DataSource.READS, DataSource.REFERENCE})

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -48,7 +48,7 @@ import java.util.Iterator;
* @author mhanna
* @version 0.1
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
public class AlignmentValidation extends ReadWalker<Integer,Integer> {
/**
* The supporting BWT index generated using BWT.

2
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -50,7 +50,7 @@ import java.util.*;
* gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here,
* the gatk engine should deal with any data related information.
*/
@DocumentedGATKFeature(groupName = "GATK Engine")
@DocumentedGATKFeature(groupName = "GATK Engine (parameters available to all tools)")
public class CommandLineGATK extends CommandLineExecutable {
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
private String analysisName = null;

2
public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
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@ -45,7 +45,7 @@ import java.util.Map;
/**
* Computes the coverage per sample for every position (use with -L argument!).
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CoverageBySample extends LocusWalker<Integer, Integer> {
@Output
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
* A SamRecordFilter that also depends on the header.
*/
@DocumentedGATKFeature(
groupName = "Read filters",
groupName = "Read Filters",
summary = "GATK Engine arguments that filter or transfer incoming SAM/BAM data files" )
public abstract class ReadFilter implements SamRecordFilter {
/**

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.List;
import java.util.Set;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
@DocumentedGATKFeature(enable = true, groupName = "Variant Annotations", summary = "Annotations available to VariantAnnotator and the variant callers (some restrictions apply)")
public abstract class VariantAnnotatorAnnotation {
// return the INFO keys
public abstract List<String> getKeyNames();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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@ -123,7 +123,7 @@ import java.io.PrintStream;
* @author Mark DePristo
* @since May 7, 2010
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@By(DataSource.REFERENCE)
public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
@Output

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
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@ -46,7 +46,7 @@ import java.util.List;
/**
* Test routine for new VariantContext object
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CompareCallableLoci extends RodWalker<List<CallableLoci.CallableBaseState>, long[][]> {
@Output
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
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@ -63,7 +63,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE})
@By(DataSource.REFERENCE)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
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@ -93,7 +93,7 @@ import java.io.PrintStream;
*
* @author Kiran Garimella, Mark DePristo
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
@Output PrintStream out;
@Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
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@ -97,7 +97,7 @@ import java.util.Map;
*
* @author Mark DePristo
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
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@ -71,7 +71,7 @@ import java.util.List;
* @author Kiran Garimela
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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@ -134,7 +134,7 @@ import java.util.List;
* @author Mark DePristo
* @since 7/4/11
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class DiffObjects extends RodWalker<Integer, Integer> {
/**
* Writes out a file of the DiffEngine format:

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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@ -81,7 +81,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceMaker extends FastaReferenceMaker {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
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@ -67,7 +67,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
@Output PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
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@ -39,7 +39,7 @@ import java.io.PrintStream;
/**
* Calculates basic statistics about the reference sequence itself
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
@Output PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
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@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountBases extends ReadWalker<Integer, Long> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
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@ -48,7 +48,7 @@ import java.util.List;
* very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
* This was its very first use.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CountIntervals extends RefWalker<Long, Long> {
@Output
PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
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@ -65,7 +65,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable {
@Output(doc="Write count to this file instead of STDOUT")
PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
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@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* Walks over the input data set, calculating the number of reads seen from male samples for diagnostic purposes.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountMales extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
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@ -73,7 +73,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>>, NanoSchedulable {
@Output
public PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
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@ -65,7 +65,7 @@ import java.util.List;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class CountRODsByRef extends RefWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> {
/**

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
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@ -66,7 +66,7 @@ import java.util.Map;
* </pre>
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
@Output (doc = "GATKReport table output")

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
View File

@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountReads extends ReadWalker<Integer, Integer> implements NanoSchedulable {
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
View File

@ -63,7 +63,7 @@ import java.util.List;
* [-L input.intervals]
* </pre>
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
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@ -72,7 +72,7 @@ import java.text.NumberFormat;
* reads with QC failure flag set, number of duplicates, percentage mapped, etc.
* @author aaron
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements NanoSchedulable {
@Output

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
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@ -54,7 +54,7 @@ import java.util.List;
* Associated command:
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class Pileup extends LocusWalker<String, Integer> implements TreeReducible<Integer>, NanoSchedulable {
private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
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@ -42,7 +42,7 @@ import java.io.PrintStream;
* Prints out all of the RODs in the input data set. Data is rendered using the toString() method
* of the given ROD.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class PrintRODs extends RodWalker<Integer, Integer> {
@Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true)
public RodBinding<Feature> input;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
View File

@ -61,7 +61,7 @@ import java.io.PrintStream;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
public class QCRef extends RefWalker<Integer, Integer> {
@Output
public PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
View File

@ -56,7 +56,7 @@ import java.util.Arrays;
* Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
* of the clipping to the output stream.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
@Output

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
View File

@ -52,7 +52,7 @@ import java.util.Arrays;
* each overlapping read, and quality score) to the reference pileup data generated by samtools. Samtools' pileup data
* should be specified using the command-line argument '-pileup:SAMPileup <your sam pileup file>'.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.READS,DataSource.REFERENCE})
public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
@Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
View File

@ -153,7 +153,7 @@ import java.util.regex.Pattern;
* @author Mark DePristo
* @since 2010
*/
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
/**

2
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
View File

@ -90,7 +90,7 @@ import java.util.*;
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@ReadTransformersMode(ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
@Requires({DataSource.READS, DataSource.REFERENCE})

2
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
View File

@ -51,7 +51,7 @@ import java.util.Map;
* Divides the input data set into separate BAM files, one for each sample in the input data set. The split
* files are named concatenating the sample name to the end of the provided outputRoot command-line argument.
*/
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
@WalkerName("SplitSamFile")
@Requires({DataSource.READS})
public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -46,8 +46,8 @@ import java.io.File;
* Time: 2:24:09 PM
*/
@DocumentedGATKFeature(
groupName = "User exceptions",
summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." )
groupName = "User Exceptions",
summary = "Errors caused by incorrect user behavior, such as bad files, bad arguments, etc." )
public class UserException extends ReviewedStingException {
/**
* The URL where people can get help messages. Printed when an error occurs

6
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
View File

@ -31,11 +31,11 @@ public class GATKDocUtils {
*/
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL;
/**
* The URL root for STABLE GATKDOC units
* The URL root for STABLE GATKDOC units //TODO: do sthing with this or remove -- URL goes nowhere
*/
public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
/**
* The URL root for UNSTABLE GATKDOC units
* The URL root for UNSTABLE GATKDOC units //TODO: do sthing with this or remove -- URL goes nowhere
*/
public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
@ -55,7 +55,7 @@ public class GATKDocUtils {
/**
* Returns a full URL http://etc/ linking to the documentation for class (assuming it
* exists). Currently points to the RELEASE doc path only.
* exists). Currently points to the RELEASE doc path only. //TODO: do sthing with other paths or remove ?
*
* @param c
* @return

4
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
View File

@ -117,8 +117,8 @@ public class GATKDoclet {
static {
STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
"Reference ordered data (ROD) codecs",
"Tribble codecs for reading reference ordered data such as VCF or BED files"));
"ROD Codecs",
"Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED"));
}