gatk-3.8/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java

package org.broadinstitute.sting.gatk;

import net.sf.samtools.SAMFileReader.ValidationStringency;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.cmdline.Option;

import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;

import java.io.*;
import java.util.HashMap;

public class GenomeAnalysisTK extends CommandLineProgram {
    // Usage and parameters
    @Usage(programVersion="0.1") public String USAGE = "SAM Validator\n";
    @Option(shortName="I", doc="SAM or BAM file for validation") public File INPUT_FILE;
    @Option(shortName="M", doc="Maximum number of reads to process before exiting", optional=true) public String MAX_READS_ARG = "-1";
    @Option(shortName="S", doc="How strict should we be with validation", optional=true) public String STRICTNESS_ARG = "strict";
    @Option(shortName="R", doc="Reference sequence file", optional=true) public File REF_FILE_ARG = null;
    @Option(shortName="B", doc="Debugging output", optional=true) public String DEBUGGING_STR = null;
    @Option(shortName="L", doc="Genome region to operation on: from chr:start-end", optional=true) public String REGION_STR = null;
    @Option(shortName="T", doc="Type of analysis to run") public String Analysis_Name = null;
    @Option(shortName="DBSNP", doc="DBSNP file", optional=true) public String DBSNP_FILE = null;
    @Option(shortName="THREADED_IO", doc="If true, enables threaded I/O operations", optional=true) public String ENABLED_THREADED_IO = "false";
    @Option(shortName="U", doc="If true, enables unsafe operations, nothing will be checked at runtime.  You better know what you are doing if you set this flag.", optional=false) public String UNSAFE = "false";
    @Option(shortName="SORT_ON_FLY", doc="If true, enables on fly sorting of reads file.", optional=false) public String ENABLED_SORT_ON_FLY = "false";

    public static HashMap<String, Object> MODULES = new HashMap<String,Object>();
    public static void addModule(final String name, final Object walker) {
        System.out.printf("* Adding module %s%n", name);
        MODULES.put(name, walker);
    }

    static {
        addModule("CountLoci", new CountLociWalker());
        addModule("Pileup", new PileupWalker());
        addModule("CountReads", new CountReadsWalker());
        addModule("PrintReads", new PrintReadsWalker());
        addModule("Base_Quality_Histogram", new BaseQualityHistoWalker());
        addModule("Aligned_Reads_Histogram", new AlignedReadsHistoWalker());
        addModule("AlleleFrequency", new AlleleFrequencyWalker());
        addModule("SingleSampleGenotyper", new SingleSampleGenotyper());
        addModule("Null", new NullWalker());
        addModule("DepthOfCoverage", new DepthOfCoverageWalker());
        addModule("CountMismatches", new MismatchCounterWalker());
    }

    private TraversalEngine engine = null;
    public boolean DEBUGGING = false;

    /** Required main method implementation. */
    public static void main(String[] argv) {
        System.exit(new GenomeAnalysisTK().instanceMain(argv));
    }

    protected int doWork() {
        final boolean TEST_ROD = false;
        ReferenceOrderedData[] rods = null;

        if ( TEST_ROD ) {
            ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class );
            gff.testMe();

            //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
            ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
            //dbsnp.testMe();
            rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
        }
        else if ( DBSNP_FILE != null ) {
            ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class );
            //dbsnp.testMe();
            rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
        }
        else {
            rods = new ReferenceOrderedData[] {}; // { gff, dbsnp };
        }

        this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods);

        ValidationStringency strictness;
    	if ( STRICTNESS_ARG == null ) {
            strictness = ValidationStringency.STRICT;
    	}
    	else if ( STRICTNESS_ARG.toLowerCase().equals("lenient") ) {
    		strictness = ValidationStringency.LENIENT;
    	}
    	else if ( STRICTNESS_ARG.toLowerCase().equals("silent") ) {
    		strictness = ValidationStringency.SILENT;
    	}
    	else {
            strictness = ValidationStringency.STRICT;
    	}
        System.err.println("Strictness is " + strictness);
        engine.setStrictness(strictness);

        engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true")));
        engine.setMaxReads(Integer.parseInt(MAX_READS_ARG));

        if ( REGION_STR != null ) {
            engine.setLocation(REGION_STR);
        }

        engine.setSafetyChecking(! UNSAFE.toLowerCase().equals("true"));
        engine.setSortOnFly(ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));

        engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
        //engine.testReference();
        
        //LocusWalker<Integer,Integer> walker = new PileupWalker();

        // Try to get the module specified
        Object my_module;
        if (MODULES.containsKey(Analysis_Name)) {
            my_module = MODULES.get(Analysis_Name);
        } else {
            System.out.println("Could not find module "+Analysis_Name);
            return 0;
        }

        try {
            LocusWalker<?, ?> walker = (LocusWalker<?, ?>)my_module;
            engine.traverseByLoci(walker);
        }
        catch ( java.lang.ClassCastException e ) {
            // I guess we're a read walker LOL
            ReadWalker<?, ?> walker = (ReadWalker<?, ?>)my_module;
            engine.traverseByRead(walker);
        }

        return 0;
    }
}