gatk-3.8/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

/*
 * Copyright (c) 2010 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,
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package org.broadinstitute.sting.gatk;

import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.walkers.Walker;

import java.util.*;

import net.sf.picard.filter.SamRecordFilter;

/**
 * @author aaron
 */
public abstract class CommandLineExecutable extends CommandLineProgram {
    /**
     * The actual engine which performs the analysis.
     */
    protected GenomeAnalysisEngine engine = new GenomeAnalysisEngine();

    // get the analysis name
    public abstract String getAnalysisName();

    /**
     * Gets the GATK argument bundle.
     * @return A structure consisting of whatever arguments should be used to initialize the GATK engine.
     */
    protected abstract GATKArgumentCollection getArgumentCollection();

    /**
     * A list of all the arguments initially used as sources.
     */
    private final Collection<Object> argumentSources = new ArrayList<Object>();

    /**
     * this is the function that the inheriting class can expect to have called
     * when the command line system has initialized.
     *
     * @return the return code to exit the program with
     */
    protected int execute() throws Exception {
        argumentSources.add(this);

        Walker<?,?> walker = engine.getWalkerByName(getAnalysisName());

        try {
            engine.setArguments(getArgumentCollection());
            engine.setWalker(walker);
            walker.setToolkit(engine);

            Collection<SamRecordFilter> filters = engine.createFilters();
            engine.setFilters(filters);

            // load the arguments into the walker / filters.
            // TODO: The fact that this extra load call exists here when all the parsing happens at the engine
            // TODO: level indicates that we're doing something wrong.  Turn this around so that the GATK can drive
            // TODO: argument processing.
            loadArgumentsIntoObject(walker);
            argumentSources.add(walker);

            for (SamRecordFilter filter: filters) {
                loadArgumentsIntoObject(filter);
                argumentSources.add(filter);
            }

            engine.execute();
            generateGATKRunReport(walker);
        } catch ( Exception e ) {
            generateGATKRunReport(walker, e);
            throw e;
        }

        // always return 0
        return 0;
    }

    /**
     * Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
     * This report will be written to either STDOUT or to the run repository, depending on the options
     * for -et.
     *
     * @param e the exception, can be null if no exception occurred
     */
    private void generateGATKRunReport(Walker<?,?> walker, Exception e) {
        if ( getArgumentCollection().phoneHomeType != GATKRunReport.PhoneHomeOption.NO_ET ) {
            GATKRunReport report = new GATKRunReport(walker, e, engine, getArgumentCollection().phoneHomeType );
            if ( getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT )
                report.postReport(System.out);
            else
                report.postReport();
        }
    }

    /**
     * Convenience method for fully parameterized generateGATKRunReport when an exception has
     * not occurred
     *
     * @param walker
     */
    private void generateGATKRunReport(Walker<?,?> walker) {
        generateGATKRunReport(walker, null);
    }

    /**
     * Subclasses of CommandLinePrograms can provide their own types of command-line arguments.
     * @return A collection of type descriptors generating implementation-dependent placeholders.
     */
    protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
        return Arrays.asList( new VCFWriterArgumentTypeDescriptor(engine,System.out,argumentSources),
                              new SAMFileReaderArgumentTypeDescriptor(engine),
                              new SAMFileWriterArgumentTypeDescriptor(engine,System.out),
                              new OutputStreamArgumentTypeDescriptor(engine,System.out) );
    }

    /**
     * GATK can add arguments dynamically based on analysis type.
     *
     * @return true
     */
    @Override
    protected boolean canAddArgumentsDynamically() {
        return true;
    }

    /**
     * GATK provides the walker as an argument source.
     * @return List of walkers to load dynamically.
     */
    @Override
    protected Class[] getArgumentSources() {
        // No walker info?  No plugins.
        if (getAnalysisName() == null) return new Class[] {};

        Collection<Class> argumentSources = new ArrayList<Class>();

        Walker walker = engine.getWalkerByName(getAnalysisName());
        engine.setArguments(getArgumentCollection());
        engine.setWalker(walker);
        walker.setToolkit(engine);
        argumentSources.add(walker.getClass());

        Collection<SamRecordFilter> filters = engine.createFilters();
        for(SamRecordFilter filter: filters)
            argumentSources.add(filter.getClass());

        Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
        return argumentSources.toArray(argumentSourcesAsArray);
    }

    @Override
    protected String getArgumentSourceName( Class argumentSource ) {
        return engine.getWalkerName((Class<Walker>)argumentSource);
    }

    /**
     * Supply command-line argument tags to the GATK engine.
     * @param key Key to use, created by the command-line argument system.
     * @param tags List of freeform tags.
     */
    @Override
    protected void addTags(Object key, List<String> tags) {
        engine.addTags(key,tags);
    }
        }