CollectMultipleMetrics.java

package picard.analysis;

import htsjdk.samtools.util.CollectionUtil;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.programgroups.Metrics;
import picard.cmdline.StandardOptionDefinitions;

import java.io.File;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;

/**
 * Class that is designed to instantiate and execute multiple metrics programs that extend
 * SinglePassSamProgram while making only a single pass through the SAM file and supplying
 * each program with the records as it goes.
 *
 * @author Tim Fennell
 */
@CommandLineProgramProperties(
        usage = "Takes an input BAM and reference sequence and runs one or more Picard " +
                "metrics modules at the same time to cut down on I/O. Currently all programs are run with " +
                "default options and fixed output extesions, but this may become more flexible in future.",
        usageShort = "A \"meta-metrics\" calculating program that produces multiple metrics for the provided SAM/BAM",
        programGroup = Metrics.class
)
public class CollectMultipleMetrics extends CommandLineProgram {

    /**
     * This interface allows developers to create Programs to run in addition to the ones defined in the Program enum.
     */
    public static interface ProgramInterface {
        SinglePassSamProgram makeInstance(final String outbase);
    }

    public static enum Program implements ProgramInterface {
        CollectAlignmentSummaryMetrics {
            @Override public SinglePassSamProgram makeInstance(final String outbase) {
                final CollectAlignmentSummaryMetrics program = new CollectAlignmentSummaryMetrics();
                program.OUTPUT = new File(outbase + ".alignment_summary_metrics");
                return program;
            }
        },
        CollectInsertSizeMetrics {
            @Override
            public SinglePassSamProgram makeInstance(final String outbase) {
                final CollectInsertSizeMetrics program = new CollectInsertSizeMetrics();
                program.OUTPUT         = new File(outbase + ".insert_size_metrics");
                program.Histogram_FILE = new File(outbase + ".insert_size_Histogram.pdf");
                return program;
            }
        },
        QualityScoreDistribution {
            public SinglePassSamProgram makeInstance(final String outbase) {
                final QualityScoreDistribution program = new QualityScoreDistribution();
                program.OUTPUT       = new File(outbase + ".quality_distribution_metrics");
                program.CHART_OUTPUT = new File(outbase + ".quality_distribution.pdf");
                return program;
            }
        },
        MeanQualityByCycle {
            public SinglePassSamProgram makeInstance(final String outbase) {
                final MeanQualityByCycle program = new MeanQualityByCycle();
                program.OUTPUT       = new File(outbase + ".quality_by_cycle_metrics");
                program.CHART_OUTPUT = new File(outbase + ".quality_by_cycle.pdf");
                return program;
            }
        },
        CollectBaseDistributionByCycle {
            public SinglePassSamProgram makeInstance(final String outbase) {
                final CollectBaseDistributionByCycle program = new CollectBaseDistributionByCycle();
                program.OUTPUT       = new File(outbase + ".base_distribution_by_cycle_metrics");
                program.CHART_OUTPUT = new File(outbase + ".base_distribution_by_cycle.pdf");
                return program;
            }
        };

    }

    @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input SAM or BAM file.")
    public File INPUT;

    @Option(shortName=StandardOptionDefinitions.REFERENCE_SHORT_NAME, doc="Reference sequence fasta.", optional=true)
    public File REFERENCE_SEQUENCE;

    @Option(doc="If true (default), then the sort order in the header file will be ignored.",
            shortName = StandardOptionDefinitions.ASSUME_SORTED_SHORT_NAME)
    public boolean ASSUME_SORTED = true;

    @Option(doc="Stop after processing N reads, mainly for debugging.")
    public int STOP_AFTER = 0;

    @Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Base name of output files.")
    public String OUTPUT;

    @Option(doc="List of metrics programs to apply during the pass through the SAM file.")
    public List<Program> PROGRAM = CollectionUtil.makeList(Program.values());

    /**
     * Contents of PROGRAM list is transferred to this list during command-line validation, so that an outside
     * developer can invoke this class programmatically and provide alternative Programs to run by calling
     * setProgramsToRun().
     */
    private List<ProgramInterface> programsToRun;

    // Stock main method
    public static void main(final String[] args) {
        new CollectMultipleMetrics().instanceMainWithExit(args);
    }

    @Override
    protected String[] customCommandLineValidation() {
        programsToRun = new ArrayList<ProgramInterface>(PROGRAM);
        return super.customCommandLineValidation();
    }

    /**
     * Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones
     * available via enum.  This must be called before doWork().
     */
    public void setProgramsToRun(List<ProgramInterface> programsToRun) {
        this.programsToRun = programsToRun;
    }

    @Override public int doWork() {
        if (OUTPUT.endsWith(".")) {
            OUTPUT = OUTPUT.substring(0, OUTPUT.length()-1);
        }

        final List<SinglePassSamProgram> programs = new ArrayList<SinglePassSamProgram>();
        for (ProgramInterface program : new HashSet<ProgramInterface>(programsToRun)) {
            SinglePassSamProgram instance = program.makeInstance(OUTPUT);

            // Generally programs should not be accessing these directly but it might make things smoother
            // to just set them anyway
            instance.INPUT = INPUT;
            instance.REFERENCE_SEQUENCE = REFERENCE_SEQUENCE;

            instance.setDefaultHeaders(getDefaultHeaders());

            programs.add(instance);
        }

        SinglePassSamProgram.makeItSo(INPUT, REFERENCE_SEQUENCE, ASSUME_SORTED, STOP_AFTER, programs);

        return 0;
    }
}