385 lines
17 KiB
Java
385 lines
17 KiB
Java
/*
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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.gatk;
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import net.sf.picard.PicardException;
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import net.sf.samtools.SAMException;
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import org.broad.tribble.TribbleException;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
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import org.broadinstitute.sting.gatk.walkers.Attribution;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.help.*;
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import org.broadinstitute.sting.utils.text.TextFormattingUtils;
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import java.util.*;
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/**
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* All command line parameters accepted by all tools in the GATK.
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*
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* <h3>Info for general users</h3>
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*
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* <p>This is a list of options and parameters that are generally available to all tools in the GATK.</p>
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*
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* <p>There may be a few restrictions, which are indicated in individual argument descriptions. For example the -BQSR
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* argument is only meant to be used with a subset of tools, and the -pedigree argument will only be effectively used
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* by a subset of tools as well. Some arguments conflict with others, and some conversely are dependent on others. This
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* is all indicated in the detailed argument descriptions, so be sure to read those in their entirety rather than just
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* skimming the one-line summaey in the table.</p>
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*
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* <h3>Info for developers</h3>
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*
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* <p>This class is the GATK engine itself, which manages map/reduce data access and runs walkers.</p>
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*
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* <p>We run command line GATK programs using this class. It gets the command line args, parses them, and hands the
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* gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here;
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* the GATK engine should deal with any data related information.</p>
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*/
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@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_ENGINE)
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public class CommandLineGATK extends CommandLineExecutable {
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/**
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* A complete list of tools (sometimes also called walkers because they "walk" through the data to perform analyses)
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* is available in the online documentation.
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*/
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@Argument(fullName = "analysis_type", shortName = "T", doc = "Name of the tool to run")
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private String analysisName = null;
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// our argument collection, the collection of command line args we accept
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@ArgumentCollection
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private GATKArgumentCollection argCollection = new GATKArgumentCollection();
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/**
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* Get pleasing info about the GATK.
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*
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* @return A list of Strings that contain pleasant info about the GATK.
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*/
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@Override
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protected ApplicationDetails getApplicationDetails() {
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return new ApplicationDetails(createApplicationHeader(),
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getAttribution(),
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ApplicationDetails.createDefaultRunningInstructions(getClass()),
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getAdditionalHelp());
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}
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@Override
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public String getAnalysisName() {
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return analysisName;
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}
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@Override
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protected GATKArgumentCollection getArgumentCollection() {
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return argCollection;
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}
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/**
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* Required main method implementation.
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*/
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public static void main(String[] argv) {
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try {
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CommandLineGATK instance = new CommandLineGATK();
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start(instance, argv);
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System.exit(CommandLineProgram.result); // todo -- this is a painful hack
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} catch (UserException e) {
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exitSystemWithUserError(e);
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} catch (TribbleException e) {
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// We can generate Tribble Exceptions in weird places when e.g. VCF genotype fields are
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// lazy loaded, so they aren't caught elsewhere and made into User Exceptions
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exitSystemWithUserError(e);
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} catch(PicardException e) {
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// TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions?
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exitSystemWithError(e);
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} catch (SAMException e) {
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checkForMaskedUserErrors(e);
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exitSystemWithSamError(e);
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} catch (OutOfMemoryError e) {
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exitSystemWithUserError(new UserException.NotEnoughMemory());
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} catch (Throwable t) {
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checkForMaskedUserErrors(t);
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exitSystemWithError(t);
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}
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}
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public static final String PICARD_TEXT_SAM_FILE_ERROR_1 = "Cannot use index file with textual SAM file";
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public static final String PICARD_TEXT_SAM_FILE_ERROR_2 = "Cannot retrieve file pointers within SAM text files";
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public static final String NO_SPACE_LEFT_ON_DEVICE_ERROR = "No space left on device";
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public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
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private static void checkForMaskedUserErrors(final Throwable t) {
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// masked out of memory error
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if ( t instanceof OutOfMemoryError )
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exitSystemWithUserError(new UserException.NotEnoughMemory());
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// masked user error
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if ( t instanceof UserException || t instanceof TribbleException )
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exitSystemWithUserError(new UserException(t.getMessage()));
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// no message means no masked error
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final String message = t.getMessage();
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if ( message == null )
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return;
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// too many open files error
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if ( message.contains("Too many open files") )
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exitSystemWithUserError(new UserException.TooManyOpenFiles());
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// malformed BAM looks like a SAM file
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if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
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exitSystemWithSamError(t);
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// can't close tribble index when writing
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if ( message.contains("Unable to close index for") )
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exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage()));
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// disk is full
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if ( message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR) )
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exitSystemWithUserError(new UserException.NoSpaceOnDevice());
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// masked error wrapped in another one
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if ( t.getCause() != null )
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checkForMaskedUserErrors(t.getCause());
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}
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/**
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* Creates the a short blurb about the GATK, copyright info, and where to get documentation.
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*
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* @return The application header.
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*/
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public static List<String> createApplicationHeader() {
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List<String> header = new ArrayList<String>();
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header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
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header.add("Copyright (c) 2010 The Broad Institute");
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header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
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return header;
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}
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public static String getVersionNumber() {
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ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
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return headerInfo.containsKey("org.broadinstitute.sting.gatk.version") ? headerInfo.getString("org.broadinstitute.sting.gatk.version") : "<unknown>";
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}
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public static String getBuildTime() {
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ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
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return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : "<unknown>";
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}
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/**
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* If the user supplied any additional attribution, return it here.
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* @return Additional attribution if supplied by the user. Empty (non-null) list otherwise.
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*/
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private List<String> getAttribution() {
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List<String> attributionLines = new ArrayList<String>();
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// If no analysis name is present, fill in extra help on the walkers.
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WalkerManager walkerManager = engine.getWalkerManager();
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String analysisName = getAnalysisName();
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if(analysisName != null && walkerManager.exists(analysisName)) {
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Class<? extends Walker> walkerType = walkerManager.getWalkerClassByName(analysisName);
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if(walkerType.isAnnotationPresent(Attribution.class))
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attributionLines.addAll(Arrays.asList(walkerType.getAnnotation(Attribution.class).value()));
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}
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return attributionLines;
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}
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/**
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* Retrieves additional information about GATK walkers.
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* the code in HelpFormatter and supply it as a helper to this method.
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*
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* @return A string summarizing the walkers available in this distribution.
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*/
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private String getAdditionalHelp() {
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String additionalHelp;
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// If no analysis name is present, fill in extra help on the walkers.
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WalkerManager walkerManager = engine.getWalkerManager();
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String analysisName = getAnalysisName();
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if(analysisName != null && walkerManager.exists(getAnalysisName()))
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additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(getAnalysisName()));
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else
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additionalHelp = getAllWalkerHelp();
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return additionalHelp;
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}
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private static final int PACKAGE_INDENT = 1;
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private static final int WALKER_INDENT = 3;
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private static final String FIELD_SEPARATOR = " ";
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private String getWalkerHelp(Class<? extends Walker> walkerType) {
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// Construct a help string to output details on this walker.
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StringBuilder additionalHelp = new StringBuilder();
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Formatter formatter = new Formatter(additionalHelp);
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formatter.format("Available Reference Ordered Data types:%n");
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formatter.format(new FeatureManager().userFriendlyListOfAvailableFeatures());
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formatter.format("%n");
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formatter.format("For a full description of this walker, see its GATKdocs at:%n");
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formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
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return additionalHelp.toString();
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}
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/**
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* Load in additional help information about all available walkers.
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* @return A string representation of the additional help.
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*/
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private String getAllWalkerHelp() {
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// Construct a help string to output available walkers.
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StringBuilder additionalHelp = new StringBuilder();
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Formatter formatter = new Formatter(additionalHelp);
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// Get the list of walker names from the walker manager.
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WalkerManager walkerManager = engine.getWalkerManager();
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// Build a list sorted by walker display name. As this information is collected, keep track of the longest
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// package / walker name for later formatting.
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SortedSet<HelpEntry> helpText = new TreeSet<HelpEntry>(new HelpEntryComparator());
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int longestPackageName = 0;
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int longestWalkerName = 0;
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for(Map.Entry<String,Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(true).entrySet()) {
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// Get the display name.
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String packageName = walkersByPackage.getKey();
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String packageDisplayName = walkerManager.getPackageDisplayName(walkersByPackage.getKey());
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String packageHelpText = walkerManager.getPackageSummaryText(packageName);
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// Compute statistics about which names is longest.
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longestPackageName = Math.max(longestPackageName,packageDisplayName.length());
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SortedSet<HelpEntry> walkersInPackage = new TreeSet<HelpEntry>(new HelpEntryComparator());
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for(Class<? extends Walker> walkerType: walkersByPackage.getValue()) {
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String walkerName = walkerType.getName();
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String walkerDisplayName = walkerManager.getName(walkerType);
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String walkerHelpText = walkerManager.getWalkerSummaryText(walkerType);
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longestWalkerName = Math.max(longestWalkerName,walkerManager.getName(walkerType).length());
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walkersInPackage.add(new HelpEntry(walkerName,walkerDisplayName,walkerHelpText));
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}
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// Dump the walkers into the sorted set.
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helpText.add(new HelpEntry(packageName,packageDisplayName,packageHelpText,Collections.unmodifiableSortedSet(walkersInPackage)));
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}
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final int headerWidth = Math.max(longestPackageName+PACKAGE_INDENT,longestWalkerName+WALKER_INDENT);
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for(HelpEntry packageHelp: helpText) {
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printDescriptorLine(formatter,PACKAGE_INDENT,packageHelp.displayName,headerWidth,FIELD_SEPARATOR,packageHelp.summary,TextFormattingUtils.DEFAULT_LINE_WIDTH);
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for(HelpEntry walkerHelp: packageHelp.children)
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printDescriptorLine(formatter,WALKER_INDENT,walkerHelp.displayName,headerWidth,FIELD_SEPARATOR,walkerHelp.summary,TextFormattingUtils.DEFAULT_LINE_WIDTH);
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// Print a blank line between sets of walkers.
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printDescriptorLine(formatter,0,"",headerWidth,FIELD_SEPARATOR,"", TextFormattingUtils.DEFAULT_LINE_WIDTH);
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}
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return additionalHelp.toString();
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}
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private void printDescriptorLine(Formatter formatter,
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int headerIndentWidth,
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String header,
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int headerWidth,
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String fieldSeparator,
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String description,
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int lineWidth) {
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final int headerPaddingWidth = headerWidth - header.length() - headerIndentWidth;
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final int descriptionWidth = lineWidth - fieldSeparator.length() - headerWidth;
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List<String> wordWrappedText = TextFormattingUtils.wordWrap(description,descriptionWidth);
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String headerIndentFormatString = headerIndentWidth > 0 ? "%" + headerIndentWidth + "s" : "%s";
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String headerPaddingFormatString = headerPaddingWidth > 0 ? "%" + headerPaddingWidth + "s" : "%s";
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String headerWidthFormatString = headerWidth > 0 ? "%" + headerWidth + "s" : "%s";
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// Output description line.
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formatter.format(headerIndentFormatString + "%s" + headerPaddingFormatString + "%s%s%n",
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"", header, "", fieldSeparator, wordWrappedText.size()>0?wordWrappedText.get(0):"");
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for(int i = 1; i < wordWrappedText.size(); i++)
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formatter.format(headerWidthFormatString + "%s%s%n", "", fieldSeparator, wordWrappedText.get(i));
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}
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}
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/**
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* Represents a given help entry; contains a display name, a summary and optionally some children.
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*/
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class HelpEntry {
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public final String uid;
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public final String displayName;
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public final String summary;
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public final SortedSet<HelpEntry> children;
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/**
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* Create a new help entry with the given display name, summary and children.
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* @param uid a unique identifier. Usually, the java package.
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* @param displayName display name for this help entry.
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* @param summary summary for this help entry.
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* @param children children for this help entry.
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*/
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public HelpEntry(String uid, String displayName, String summary, SortedSet<HelpEntry> children) {
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this.uid = uid;
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this.displayName = displayName;
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this.summary = summary;
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this.children = children;
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}
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/**
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* Create a new help entry with the given display name, summary and children.
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* @param uid a unique identifier. Usually, the java package.
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* @param displayName display name for this help entry.
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* @param summary summary for this help entry.
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*/
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public HelpEntry(String uid, String displayName, String summary) {
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this(uid,displayName,summary,null);
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}
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}
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/**
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* Compare two help entries by display name.
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*/
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class HelpEntryComparator implements Comparator<HelpEntry> {
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private static TextFormattingUtils.CaseInsensitiveComparator textComparator = new TextFormattingUtils.CaseInsensitiveComparator();
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/**
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* Compares the order of lhs to rhs, not taking case into account.
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* @param lhs First object to compare.
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* @param rhs Second object to compare.
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* @return 0 if objects are identical; -1 if lhs is before rhs, 1 if rhs is before lhs. Nulls are treated as after everything else.
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*/
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public int compare(HelpEntry lhs, HelpEntry rhs) {
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if(lhs == null && rhs == null) return 0;
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if(lhs == null || lhs.displayName.equals("")) return 1;
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if(rhs == null || rhs.displayName.equals("")) return -1;
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return lhs.displayName.equals(rhs.displayName) ? textComparator.compare(lhs.uid,rhs.uid) : textComparator.compare(lhs.displayName,rhs.displayName);
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}
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} |