Created ListAnnotations utility (extends CommandLineProgram)
--Refactored listAnnotations basic method out of VA into HelpUtils --HelpUtils.listAnnotations() is now called by both VA and the new ListAnnotations utility (lives in sting.tools) --This way we keep the VA --list option but we also offer a way to list annotations without a full valid VA command-line, which was a pain users continually complained about --We could get rid of the VA --list option altogether ...?
This commit is contained in:
Geraldine Van der Auwera
parent
95a9ed853d
commit
6b4d88ebe9
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@ -36,10 +36,10 @@ 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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@ -47,7 +47,6 @@ import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
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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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@ -165,7 +164,7 @@ 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 +176,7 @@ 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 +184,14 @@ 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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HelpUtils.listAnnotations();
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System.exit(0);
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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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@ -35,7 +35,6 @@ import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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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.variant.bcf2.BCF2Codec;
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@ -54,7 +53,7 @@ import java.util.*;
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/**
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*
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* Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples.
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* Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples
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*
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* <p>
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* The main purpose of this tool is to speed up the gather function when using scatter-gather parallelization.
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@ -80,10 +79,14 @@ import java.util.*;
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* A combined VCF. The output file should be 'name.vcf' or 'name.VCF'.
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* <\p>
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*
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* <h3>Important note</h3>
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* <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
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* invoke it is a little different from other GATK tools (see example below), and it does not accept any of the
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* classic "CommandLineGATK" arguments.</p>
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*
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* <h3>Examples</h3>
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* <h3>Example</h3>
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* <pre>
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* java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
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* java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
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* -R ref.fasta \
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* -V input1.vcf \
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* -V input2.vcf \
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@ -95,7 +98,7 @@ import java.util.*;
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* @since Jan 2012
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP )
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public class CatVariants extends CommandLineProgram {
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// setup the logging system, used by some codecs
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private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getRootLogger();
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@ -124,7 +127,7 @@ public class CatVariants extends CommandLineProgram {
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* print usage information
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*/
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private static void printUsage() {
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System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
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System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
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System.err.println(" The input files can be of type: VCF (ends in .vcf or .VCF)");
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System.err.println(" BCF2 (ends in .bcf or .BCF)");
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System.err.println(" Output file must be vcf or bcf file (.vcf or .bcf)");
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@ -0,0 +1,85 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.tools;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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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.help.HelpUtils;
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/**
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* Utility program to print a list of available annotations
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*
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* <p>This is a very simple utility tool that retrieves available annotations for use with tools such as
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* UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.</p>
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*
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* <h3>Important note</h3>
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* <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
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* invoke it is a little different from other GATK tools (see usage below), and it does not accept any of the
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* classic "CommandLineGATK" arguments.</p>
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*
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* <h3>Usage</h3>
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* <pre>java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations</pre>
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*
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* @author vdauwera
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* @since 3/14/13
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_HELPUTILS )
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public class ListAnnotations extends CommandLineProgram {
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/*
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* Print usage information
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*
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* TODO: would be more convenient if we could just call the program by name instead of the full classpath
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*/
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private static void printUsage() {
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System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations");
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System.err.println(" Prints a list of available annotations and exits.");
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}
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// TODO: override CommandLineProgram bit that offers version, logging etc arguments. We don't need that stuff here and it makes the doc confusing.
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@Override
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protected int execute() throws Exception {
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HelpUtils.listAnnotations();
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return 0;
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}
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public static void main(String[] args){
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try {
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ListAnnotations instance = new ListAnnotations();
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start(instance, args);
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System.exit(CommandLineProgram.result);
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} catch ( UserException e ) {
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printUsage();
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exitSystemWithUserError(e);
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} catch ( Exception e ) {
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exitSystemWithError(e);
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}
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}
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}
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@ -56,6 +56,7 @@ public class HelpConstants {
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public final static String DOCS_CAT_VARDISC = "Variant Discovery Tools";
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public final static String DOCS_CAT_VARMANIP = "Variant Evaluation and Manipulation Tools";
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public final static String DOCS_CAT_TEST = "Testing Tools";
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public final static String DOCS_CAT_HELPUTILS = "Help Utilities";
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public static String forumPost(String post) {
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return GATK_FORUM_URL + post;
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@ -28,9 +28,15 @@ package org.broadinstitute.sting.utils.help;
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import com.sun.javadoc.FieldDoc;
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import com.sun.javadoc.PackageDoc;
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import com.sun.javadoc.ProgramElementDoc;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import java.lang.reflect.Field;
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import java.util.List;
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public class HelpUtils {
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@ -70,4 +76,27 @@ public class HelpUtils {
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String.format("%s", doc.name());
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}
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/**
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* Simple method to print a list of available annotations.
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*/
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public static void listAnnotations() {
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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:");
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System.out.println("http://www.broadinstitute.org/gatk/gatkdocs/");
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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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}
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}
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