Merge pull request #117 from broadinstitute/gg_handling_deprecated_tools_45941819
gg handling deprecated tools 45941819
This commit is contained in:
MauricioCarneiro
commit
470746c907
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@ -70,10 +70,11 @@ import java.util.Map;
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/**
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* Total (unfiltered) depth over all samples.
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*
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* While the sample-level (FORMAT) DP field describes the total depth of reads that passed the Unified Genotyper's
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* <p>While the sample-level (FORMAT) DP field describes the total depth of reads that passed the caller's
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* internal quality control metrics (like MAPQ > 17, for example), the INFO field DP represents the unfiltered depth
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* over all samples. Note though that the DP is affected by downsampling (-dcov), so the max value one can obtain for
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* N samples with -dcov D is N * D
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* </p>
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*/
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public class Coverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
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@ -69,10 +69,15 @@ import java.util.*;
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/**
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* Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
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* being seen on only the forward or only the reverse strand) in the reads? More bias is
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* indicative of false positive calls. Note that the fisher strand test may not be
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* calculated for certain complex indel cases or for multi-allelic sites.
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* Phred-scaled p-value using Fisher's Exact Test to detect strand bias
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*
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* <p>Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
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* being seen on only the forward or only the reverse strand) in the reads. More bias is
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* indicative of false positive calls.
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* </p>
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*
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* <h3>Caveat</h3>
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* <p>The Fisher Strand test may not be calculated for certain complex indel cases or for multi-allelic sites.</p>
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*/
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public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
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private final static Logger logger = Logger.getLogger(FisherStrand.class);
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@ -68,7 +68,7 @@ import java.util.Map;
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/**
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* GC content of the reference around this site
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* GC content of the reference around the given site
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*
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* <p>The GC content is the number of GC bases relative to the total number of bases (# GC bases / # all bases) around this site on the reference.</p>
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*
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@ -61,7 +61,7 @@ import java.util.List;
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* User: rpoplin
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* Date: Nov 27, 2009
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*
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* A collection of the arguments that are common to both CovariateCounterWalker and TableRecalibrationWalker.
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* A collection of the arguments that are used for BQSR. Used to be common to both CovariateCounterWalker and TableRecalibrationWalker.
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* This set of arguments will also be passed to the constructor of every Covariate when it is instantiated.
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*/
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@ -131,14 +131,14 @@ public class RecalibrationArgumentCollection {
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public boolean RUN_WITHOUT_DBSNP = false;
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/**
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* CountCovariates and TableRecalibration accept a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
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* BaseRecalibrator accepts a --solid_recal_mode <MODE> flag which governs how the recalibrator handles the
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* reads which have had the reference inserted because of color space inconsistencies.
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*/
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@Argument(fullName = "solid_recal_mode", shortName = "sMode", required = false, doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS")
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public RecalUtils.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.SET_Q_ZERO;
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/**
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* CountCovariates and TableRecalibration accept a --solid_nocall_strategy <MODE> flag which governs how the recalibrator handles
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* BaseRecalibrator accepts a --solid_nocall_strategy <MODE> flag which governs how the recalibrator handles
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* no calls in the color space tag. Unfortunately because of the reference inserted bases mentioned above, reads with no calls in
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* their color space tag can not be recalibrated.
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*/
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@ -47,6 +47,7 @@
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package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.filters.*;
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@ -55,18 +56,27 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.report.GATKReportTable;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import org.broadinstitute.sting.utils.recalibration.*;
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import java.io.*;
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/**
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* Evaluate the performance of the base recalibration process
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*
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* <p>This tool aims to evaluate the results of the Base Quality Score Recalibration (BQSR) process.</p>
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*
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* <h3>Caveat</h3>
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* <p>This tool is currently experimental. We do not provide documentation nor support for its operation.</p>
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*
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
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@PartitionBy(PartitionType.READ)
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public class RecalibrationPerformance extends RodWalker<Integer, Integer> implements NanoSchedulable {
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@Output(doc="Write output to this file")
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@Output
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public PrintStream out;
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@Input(fullName="recal", shortName="recal", required=false, doc="The input covariates table file")
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@ -48,6 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -55,6 +56,8 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import java.io.PrintStream;
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import java.util.ArrayList;
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@ -63,11 +66,11 @@ import java.util.LinkedList;
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import java.util.Map;
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/**
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* Simple walker to plot the coverage distribution per base.
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* Simple walker to plot the coverage distribution per base
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*
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* <p>
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* Features of this walker:
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* <li>includes a smart counting of uncovered bases without visiting the uncovered loci.</li>
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* <li>includes a smart counting of uncovered bases without visiting the uncovered loci</li>
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* <li>includes reads with deletions in the loci (optionally can be turned off)</li>
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* </p>
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*
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@ -91,10 +94,11 @@ import java.util.Map;
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* -fd \
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* -o report.grp
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* </pre>
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* User: carneiro
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* Date: 1/27/13
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* Time: 11:16 AM
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*
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* @author carneiro
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* @since 1/27/13
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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public class BaseCoverageDistribution extends LocusWalker<ArrayList<Integer>, Map<Integer, ArrayList<Long>>> {
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/**
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* The output GATK Report table
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@ -82,7 +82,7 @@ import java.util.*;
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*
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* This helper class holds the data HashMap as well as submaps that represent the marginal distributions collapsed over all needed dimensions.
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* It also has static methods that are used to perform the various solid recalibration modes that attempt to correct the reference bias.
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* This class holds the parsing methods that are shared between CountCovariates and TableRecalibration.
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* This class holds the parsing methods that are shared between BaseRecalibrator and PrintReads.
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*/
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public class RecalUtils {
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@ -67,6 +67,9 @@ import java.io.File;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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import static org.broadinstitute.sting.utils.DeprecatedToolChecks.getWalkerDeprecationInfo;
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import static org.broadinstitute.sting.utils.DeprecatedToolChecks.isDeprecatedWalker;
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/**
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* A GenomeAnalysisEngine that runs a specified walker.
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*/
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@ -288,40 +291,6 @@ public class GenomeAnalysisEngine {
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//return result;
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}
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// TODO -- Let's move this to a utility class in unstable - but which one?
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// **************************************************************************************
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// * Handle Deprecated Walkers *
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// **************************************************************************************
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// Mapping from walker name to major version number where the walker first disappeared
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private static Map<String, String> deprecatedGATKWalkers = new HashMap<String, String>();
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static {
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deprecatedGATKWalkers.put("CountCovariates", "2.0");
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deprecatedGATKWalkers.put("TableRecalibration", "2.0");
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deprecatedGATKWalkers.put("AlignmentWalker", "2.2");
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deprecatedGATKWalkers.put("CountBestAlignments", "2.2");
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}
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/**
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* Utility method to check whether a given walker has been deprecated in a previous GATK release
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static boolean isDeprecatedWalker(final String walkerName) {
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return deprecatedGATKWalkers.containsKey(walkerName);
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}
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/**
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* Utility method to check whether a given walker has been deprecated in a previous GATK release
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static String getDeprecatedMajorVersionNumber(final String walkerName) {
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return deprecatedGATKWalkers.get(walkerName);
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}
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// **************************************************************************************
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/**
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* Retrieves an instance of the walker based on the walker name.
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*
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@ -333,7 +302,7 @@ public class GenomeAnalysisEngine {
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return walkerManager.createByName(walkerName);
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} catch ( UserException e ) {
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if ( isDeprecatedWalker(walkerName) ) {
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e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
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e = new UserException.DeprecatedWalker(walkerName, getWalkerDeprecationInfo(walkerName));
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}
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throw e;
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}
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@ -565,6 +534,8 @@ public class GenomeAnalysisEngine {
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if ( intervals != null && intervals.isEmpty() ) {
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logger.warn("The given combination of -L and -XL options results in an empty set. No intervals to process.");
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}
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// TODO: add a check for ActiveRegion walkers to prevent users from passing an entire contig/chromosome
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}
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/**
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@ -36,18 +36,18 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
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import org.broadinstitute.sting.utils.help.HelpConstants;
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import org.broadinstitute.sting.utils.help.HelpUtils;
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import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.variant.vcf.*;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
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import it.unimi.dsi.fastutil.objects.ObjectOpenHashSet;
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import java.util.*;
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/**
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* Annotates variant calls with context information.
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*
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@ -156,7 +156,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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* If multiple records in the rod overlap the given position, one is chosen arbitrarily.
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*/
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@Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls; see documentation for more details", required=false)
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protected List<String> expressionsToUse = new ArrayList<String>();
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protected Set<String> expressionsToUse = new ObjectOpenHashSet();
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/**
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* Note that the -XL argument can be used along with this one to exclude annotations.
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@ -165,7 +165,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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protected Boolean USE_ALL_ANNOTATIONS = false;
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/**
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* Note that the --list argument requires a fully resolved and correct command-line to work.
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* Note that the --list argument requires a fully resolved and correct command-line to work. As a simpler alternative, you can use ListAnnotations (see Help Utilities).
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*/
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@Argument(fullName="list", shortName="ls", doc="List the available annotations and exit", required=false)
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protected Boolean LIST = false;
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@ -177,7 +177,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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protected Boolean ALWAYS_APPEND_DBSNP_ID = false;
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public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; }
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@Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
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@Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality threshold in order to annotate mendelian violation ratio")
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public double minGenotypeQualityP = 0.0;
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@Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false)
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@ -185,33 +185,15 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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private VariantAnnotatorEngine engine;
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private void listAnnotationsAndExit() {
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System.out.println("\nStandard annotations in the list below are marked with a '*'.");
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List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
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System.out.println("\nAvailable annotations for the VCF INFO field:");
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for (int i = 0; i < infoAnnotationClasses.size(); i++)
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System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
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System.out.println();
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List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
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System.out.println("\nAvailable annotations for the VCF FORMAT field:");
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for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
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System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
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System.out.println();
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System.out.println("\nAvailable classes/groups of annotations:");
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for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )
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System.out.println("\t" + c.getSimpleName());
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System.out.println();
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System.exit(0);
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}
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/**
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* Prepare the output file and the list of available features.
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*/
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public void initialize() {
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if ( LIST )
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listAnnotationsAndExit();
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if ( LIST ) {
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HelpUtils.listAnnotations();
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System.exit(0);
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}
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// get the list of all sample names from the variant VCF input rod, if applicable
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List<String> rodName = Arrays.asList(variantCollection.variants.getName());
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@ -104,7 +104,7 @@ public class VariantAnnotatorEngine {
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}
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// select specific expressions to use
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public void initializeExpressions(List<String> expressionsToUse) {
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public void initializeExpressions(Set<String> expressionsToUse) {
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// set up the expressions
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for ( String expression : expressionsToUse )
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requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
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@ -25,6 +25,7 @@
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package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
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import org.broadinstitute.sting.utils.DeprecatedToolChecks;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -58,7 +59,7 @@ public class AnnotationInterfaceManager {
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if ( interfaceClass == null )
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interfaceClass = classMap.get(group + "Annotation");
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if ( interfaceClass == null )
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throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly");
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throw new UserException.BadArgumentValue("group", "Annotation group " + group + " was not found; please check that you have specified the group name correctly");
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}
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}
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@ -67,8 +68,13 @@ public class AnnotationInterfaceManager {
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Class annotationClass = classMap.get(annotation);
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if ( annotationClass == null )
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annotationClass = classMap.get(annotation + "Annotation");
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if ( annotationClass == null )
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throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly");
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if ( annotationClass == null ) {
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if (DeprecatedToolChecks.isDeprecatedAnnotation(annotation) ) {
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throw new UserException.DeprecatedAnnotation(annotation, DeprecatedToolChecks.getAnnotationDeprecationInfo(annotation));
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} else {
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throw new UserException.BadArgumentValue("annotation", "Annotation " + annotation + " was not found; please check that you have specified the annotation name correctly");
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}
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}
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}
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}
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@ -117,7 +117,7 @@ import java.util.*;
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// todo -- alter logarithmic scaling to spread out bins more
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// todo -- allow for user to set linear binning (default is logarithmic)
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// todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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@By(DataSource.REFERENCE)
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@PartitionBy(PartitionType.NONE)
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@Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
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|
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@ -29,12 +29,15 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics;
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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;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.HelpConstants;
|
||||
import org.broadinstitute.variant.variantcontext.Genotype;
|
||||
import org.broadinstitute.variant.variantcontext.GenotypesContext;
|
||||
import org.broadinstitute.variant.variantcontext.VariantContext;
|
||||
|
|
@ -44,12 +47,15 @@ import java.io.*;
|
|||
import java.util.Collection;
|
||||
|
||||
/**
|
||||
* print intervals file with all the variant sites that have "most" ( >= 90% by default) of the samples with "good" (>= 10 by default)coverage ("most" and "good" can be set in the command line).
|
||||
* Print intervals file with all the variant sites for which most of the samples have good coverage
|
||||
*
|
||||
* <p>
|
||||
* CoveredByNSamplesSites is a GATK tool for filter out sites based on their coverage.
|
||||
* CoveredByNSamplesSites is a GATK tool for filtering out sites based on their coverage.
|
||||
* The sites that pass the filter are printed out to an intervals file.
|
||||
*
|
||||
* See argument defaults for what constitutes "most" samples and "good" coverage. These parameters can be modified from the command line.
|
||||
* </p>
|
||||
*
|
||||
* <h3>Input</h3>
|
||||
* <p>
|
||||
* A variant file and optionally min coverage and sample percentage values.
|
||||
|
|
@ -60,7 +66,7 @@ import java.util.Collection;
|
|||
* An intervals file.
|
||||
* </p>
|
||||
*
|
||||
* <h3>Examples</h3>
|
||||
* <h3>Example</h3>
|
||||
* <pre>
|
||||
* java -Xmx2g -jar GenomeAnalysisTK.jar \
|
||||
* -R ref.fasta \
|
||||
|
|
@ -71,7 +77,7 @@ import java.util.Collection;
|
|||
* </pre>
|
||||
*
|
||||
*/
|
||||
|
||||
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
|
||||
@By(DataSource.REFERENCE_ORDERED_DATA)
|
||||
public class CoveredByNSamplesSites extends RodWalker<GenomeLoc, Integer> implements TreeReducible<Integer> {
|
||||
|
||||
|
|
|
|||
|
|
@ -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.refdata.RefMetaDataTracker;
|
||||
|
|
@ -33,6 +34,8 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
|
|||
import org.broadinstitute.sting.gatk.report.GATKReportTable;
|
||||
import org.broadinstitute.sting.gatk.walkers.RodWalker;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.HelpConstants;
|
||||
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
|
||||
import org.broadinstitute.variant.variantcontext.*;
|
||||
import org.broadinstitute.variant.vcf.VCFHeader;
|
||||
|
|
@ -41,29 +44,30 @@ import java.io.PrintStream;
|
|||
import java.util.*;
|
||||
|
||||
/**
|
||||
* A simple walker for performing genotype concordance calculations between two callsets. Outputs a GATK table with
|
||||
* per-sample and aggregate counts and frequencies, a summary table for NRD/NRS, and a table for site allele overlaps.
|
||||
* Genotype concordance (per-sample and aggregate counts and frequencies, NRD/NRS and site allele overlaps) between two callsets
|
||||
*
|
||||
* <p>
|
||||
* Genotype concordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles,
|
||||
* GenotypeConcordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles,
|
||||
* and for each sample, the genotype-by-genotype counts (for instance, the number of sites at which a sample was
|
||||
* called homozygous reference in the EVAL callset, but homozygous variant in the COMP callset). It outputs these
|
||||
* counts as well as convenient proportions (such as the proportion of het calls in the EVAL which were called REF in
|
||||
* the COMP) and metrics (such as NRD and NRS).
|
||||
*
|
||||
* <h2> INPUT </h2>
|
||||
* <h3>Input</h3>
|
||||
* <p>
|
||||
* Genotype concordance requires two callsets (as it does a comparison): an EVAL and a COMP callset, specified via
|
||||
* the -eval and -comp arguments
|
||||
* <p>
|
||||
* the -eval and -comp arguments.
|
||||
*
|
||||
* (Optional) Jexl expressions for genotype-level filtering of EVAL or COMP genotypes, specified via the -gfe and
|
||||
* -cfe arguments, respectively.
|
||||
* </p>
|
||||
*
|
||||
* <h2> OUTPUT </h2>
|
||||
* Genotype Concordance writes a GATK report to the specified (via -o) file, consisting of multiple tables of counts
|
||||
* <h3>Output</h3>
|
||||
* Genotype Concordance writes a GATK report to the specified file (via -o) , consisting of multiple tables of counts
|
||||
* and proportions. These tables may be optionally moltenized via the -moltenize argument.
|
||||
*
|
||||
*/
|
||||
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
|
||||
public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,VariantContext>>,ConcordanceMetrics> {
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -35,7 +35,6 @@ import org.broadinstitute.sting.commandline.Argument;
|
|||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.commandline.CommandLineProgram;
|
||||
import org.broadinstitute.sting.gatk.CommandLineGATK;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.HelpConstants;
|
||||
import org.broadinstitute.variant.bcf2.BCF2Codec;
|
||||
|
|
@ -54,7 +53,7 @@ import java.util.*;
|
|||
|
||||
/**
|
||||
*
|
||||
* Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples.
|
||||
* Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples
|
||||
*
|
||||
* <p>
|
||||
* The main purpose of this tool is to speed up the gather function when using scatter-gather parallelization.
|
||||
|
|
@ -80,10 +79,14 @@ import java.util.*;
|
|||
* A combined VCF. The output file should be 'name.vcf' or 'name.VCF'.
|
||||
* <\p>
|
||||
*
|
||||
* <h3>Important note</h3>
|
||||
* <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
|
||||
* invoke it is a little different from other GATK tools (see example below), and it does not accept any of the
|
||||
* classic "CommandLineGATK" arguments.</p>
|
||||
*
|
||||
* <h3>Examples</h3>
|
||||
* <h3>Example</h3>
|
||||
* <pre>
|
||||
* java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
|
||||
* java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
|
||||
* -R ref.fasta \
|
||||
* -V input1.vcf \
|
||||
* -V input2.vcf \
|
||||
|
|
@ -95,7 +98,7 @@ import java.util.*;
|
|||
* @since Jan 2012
|
||||
*/
|
||||
|
||||
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
|
||||
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP )
|
||||
public class CatVariants extends CommandLineProgram {
|
||||
// setup the logging system, used by some codecs
|
||||
private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getRootLogger();
|
||||
|
|
@ -124,7 +127,7 @@ public class CatVariants extends CommandLineProgram {
|
|||
* print usage information
|
||||
*/
|
||||
private static void printUsage() {
|
||||
System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
|
||||
System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
|
||||
System.err.println(" The input files can be of type: VCF (ends in .vcf or .VCF)");
|
||||
System.err.println(" BCF2 (ends in .bcf or .BCF)");
|
||||
System.err.println(" Output file must be vcf or bcf file (.vcf or .bcf)");
|
||||
|
|
|
|||
|
|
@ -0,0 +1,85 @@
|
|||
/*
|
||||
* Copyright (c) 2012 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.tools;
|
||||
|
||||
import org.broadinstitute.sting.commandline.CommandLineProgram;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.sting.utils.help.HelpConstants;
|
||||
import org.broadinstitute.sting.utils.help.HelpUtils;
|
||||
|
||||
/**
|
||||
* Utility program to print a list of available annotations
|
||||
*
|
||||
* <p>This is a very simple utility tool that retrieves available annotations for use with tools such as
|
||||
* UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.</p>
|
||||
*
|
||||
* <h3>Important note</h3>
|
||||
* <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
|
||||
* invoke it is a little different from other GATK tools (see usage below), and it does not accept any of the
|
||||
* classic "CommandLineGATK" arguments.</p>
|
||||
*
|
||||
* <h3>Usage</h3>
|
||||
* <pre>java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations</pre>
|
||||
*
|
||||
* @author vdauwera
|
||||
* @since 3/14/13
|
||||
*/
|
||||
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_HELPUTILS )
|
||||
public class ListAnnotations extends CommandLineProgram {
|
||||
|
||||
/*
|
||||
* Print usage information
|
||||
*
|
||||
* TODO: would be more convenient if we could just call the program by name instead of the full classpath
|
||||
*/
|
||||
private static void printUsage() {
|
||||
System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations");
|
||||
System.err.println(" Prints a list of available annotations and exits.");
|
||||
}
|
||||
|
||||
// TODO: override CommandLineProgram bit that offers version, logging etc arguments. We don't need that stuff here and it makes the doc confusing.
|
||||
|
||||
@Override
|
||||
protected int execute() throws Exception {
|
||||
|
||||
HelpUtils.listAnnotations();
|
||||
return 0;
|
||||
}
|
||||
|
||||
public static void main(String[] args){
|
||||
try {
|
||||
ListAnnotations instance = new ListAnnotations();
|
||||
start(instance, args);
|
||||
System.exit(CommandLineProgram.result);
|
||||
} catch ( UserException e ) {
|
||||
printUsage();
|
||||
exitSystemWithUserError(e);
|
||||
} catch ( Exception e ) {
|
||||
exitSystemWithError(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,95 @@
|
|||
/*
|
||||
* Copyright (c) 2012 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.utils;
|
||||
|
||||
import it.unimi.dsi.fastutil.objects.Object2ObjectMap;
|
||||
import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* Utility class for handling deprecated tools gracefully
|
||||
*
|
||||
* @author vdauwera
|
||||
* @since 3/11/13
|
||||
*/
|
||||
public class DeprecatedToolChecks {
|
||||
|
||||
// Mapping from walker name to major version number where the walker first disappeared and optional replacement options
|
||||
private static Object2ObjectMap deprecatedGATKWalkers = new Object2ObjectOpenHashMap();
|
||||
static {
|
||||
// Indicate recommended replacement in parentheses if applicable
|
||||
deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
|
||||
deprecatedGATKWalkers.put("AnalyzeCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
|
||||
deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
|
||||
deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
|
||||
deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");
|
||||
}
|
||||
|
||||
// Mapping from walker name to major version number where the walker first disappeared and optional replacement options
|
||||
private static Object2ObjectMap deprecatedGATKAnnotations = new Object2ObjectOpenHashMap();
|
||||
static {
|
||||
// Same comments as for walkers
|
||||
deprecatedGATKAnnotations.put("DepthOfCoverage", "2.4 (renamed to Coverage)");
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method to check whether a given walker has been deprecated in a previous GATK release
|
||||
*
|
||||
* @param walkerName the walker class name (not the full package) to check
|
||||
*/
|
||||
public static boolean isDeprecatedWalker(final String walkerName) {
|
||||
return deprecatedGATKWalkers.containsKey(walkerName);
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method to check whether a given annotation has been deprecated in a previous GATK release
|
||||
*
|
||||
* @param annotationName the annotation class name (not the full package) to check
|
||||
*/
|
||||
public static boolean isDeprecatedAnnotation(final String annotationName) {
|
||||
return deprecatedGATKAnnotations.containsKey(annotationName);
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method to pull up the version number at which a walker was deprecated and the suggested replacement, if any
|
||||
*
|
||||
* @param walkerName the walker class name (not the full package) to check
|
||||
*/
|
||||
public static String getWalkerDeprecationInfo(final String walkerName) {
|
||||
return deprecatedGATKWalkers.get(walkerName).toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method to pull up the version number at which an annotation was deprecated and the suggested replacement, if any
|
||||
*
|
||||
* @param annotationName the annotation class name (not the full package) to check
|
||||
*/
|
||||
public static String getAnnotationDeprecationInfo(final String annotationName) {
|
||||
return deprecatedGATKAnnotations.get(annotationName).toString();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -371,14 +371,18 @@ public class UserException extends ReviewedStingException {
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
public static class DeprecatedWalker extends UserException {
|
||||
public DeprecatedWalker(String walkerName, String version) {
|
||||
super(String.format("Walker %s is no longer available in the GATK; it has been deprecated since version %s", walkerName, version));
|
||||
}
|
||||
}
|
||||
|
||||
public static class DeprecatedAnnotation extends UserException {
|
||||
public DeprecatedAnnotation(String annotationName, String version) {
|
||||
super(String.format("Annotation %s is no longer available in the GATK; it has been deprecated since version %s", annotationName, version));
|
||||
}
|
||||
}
|
||||
|
||||
public static class CannotExecuteQScript extends UserException {
|
||||
public CannotExecuteQScript(String message) {
|
||||
super(String.format("Unable to execute QScript: " + message));
|
||||
|
|
|
|||
|
|
@ -56,6 +56,7 @@ public class HelpConstants {
|
|||
public final static String DOCS_CAT_VARDISC = "Variant Discovery Tools";
|
||||
public final static String DOCS_CAT_VARMANIP = "Variant Evaluation and Manipulation Tools";
|
||||
public final static String DOCS_CAT_TEST = "Testing Tools";
|
||||
public final static String DOCS_CAT_HELPUTILS = "Help Utilities";
|
||||
|
||||
public static String forumPost(String post) {
|
||||
return GATK_FORUM_URL + post;
|
||||
|
|
|
|||
|
|
@ -28,9 +28,15 @@ package org.broadinstitute.sting.utils.help;
|
|||
import com.sun.javadoc.FieldDoc;
|
||||
import com.sun.javadoc.PackageDoc;
|
||||
import com.sun.javadoc.ProgramElementDoc;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
|
||||
import org.broadinstitute.sting.utils.classloader.JVMUtils;
|
||||
import org.broadinstitute.sting.utils.classloader.PluginManager;
|
||||
|
||||
import java.lang.reflect.Field;
|
||||
import java.util.List;
|
||||
|
||||
public class HelpUtils {
|
||||
|
||||
|
|
@ -70,4 +76,27 @@ public class HelpUtils {
|
|||
String.format("%s", doc.name());
|
||||
}
|
||||
|
||||
/**
|
||||
* Simple method to print a list of available annotations.
|
||||
*/
|
||||
public static void listAnnotations() {
|
||||
System.out.println("\nThis is a list of available Variant Annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator. Please see the Technical Documentation for more details about these annotations:");
|
||||
System.out.println("http://www.broadinstitute.org/gatk/gatkdocs/");
|
||||
System.out.println("\nStandard annotations in the list below are marked with a '*'.");
|
||||
List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
|
||||
System.out.println("\nAvailable annotations for the VCF INFO field:");
|
||||
for (int i = 0; i < infoAnnotationClasses.size(); i++)
|
||||
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
|
||||
System.out.println();
|
||||
List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
|
||||
System.out.println("\nAvailable annotations for the VCF FORMAT field:");
|
||||
for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
|
||||
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
|
||||
System.out.println();
|
||||
System.out.println("\nAvailable classes/groups of annotations:");
|
||||
for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )
|
||||
System.out.println("\t" + c.getSimpleName());
|
||||
System.out.println();
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue