org.broadinstitute.hellbender.tools.sv.stratify.SVStratificationEngineArgumentsCollection Maven / Gradle / Ivy

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package org.broadinstitute.hellbender.tools.sv.stratify;

import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.hellbender.engine.GATKPath;
import org.broadinstitute.hellbender.utils.tsv.TableUtils;

import java.io.Serializable;
import java.util.List;

/**
 * Arguments for use with {@link SVStatificationEngine}.
 */
public class SVStratificationEngineArgumentsCollection implements Serializable {
    // Command-line arguments
    public static final String STRATIFY_CONFIG_FILE_LONG_NAME = "stratify-config";
    public static final String TRACK_NAME_FILE_LONG_NAME = "track-name";
    public static final String TRACK_INTERVAL_FILE_LONG_NAME = "track-intervals";
    public static final String OVERLAP_FRACTION_LONG_NAME = "stratify-overlap-fraction";
    public static final String NUM_BREAKPOINT_OVERLAPS_LONG_NAME = "stratify-num-breakpoint-overlaps";
    public static final String NUM_BREAKPOINT_INTERCHROM_OVERLAPS_LONG_NAME = "stratify-num-breakpoint-overlaps-interchromosomal";
    private static final long serialVersionUID = 1L;

    /**
     * Expected format is tab-delimited and contains columns NAME, SVTYPE, MIN_SIZE, MAX_SIZE, track. First line must
     * be a header with column names. Comment lines starting with {@link TableUtils#COMMENT_PREFIX} are ignored.
     */
    @Argument(
            doc = "Stratification configuration file (.tsv)",
            fullName = STRATIFY_CONFIG_FILE_LONG_NAME
    )
    public GATKPath configFile;

    @Argument(
            doc = "Track intervals file. Can be specified multiple times.",
            fullName = TRACK_INTERVAL_FILE_LONG_NAME,
            optional = true
    )
    public List trackFileList;

    @Argument(
            doc = "Track names. Must be once for each --" + TRACK_INTERVAL_FILE_LONG_NAME,
            fullName = TRACK_NAME_FILE_LONG_NAME,
            optional = true
    )
    public List trackNameList;

    @Argument(
            doc = "Minimum overlap fraction for tracks",
            minValue = 0,
            maxValue = 1,
            fullName = OVERLAP_FRACTION_LONG_NAME
    )
    public double overlapFraction = 0;

    @Argument(
            doc = "Minimum number of variant endpoint overlaps for tracks",
            minValue = 0,
            maxValue = 2,
            fullName = NUM_BREAKPOINT_OVERLAPS_LONG_NAME
    )
    public int numBreakpointOverlaps = 1;

    @Argument(
            doc = "Minimum number of breakpoint overlaps for tracks for interchromosomal variants (e.g. BNDs)",
            minValue = 1,
            maxValue = 2,
            fullName = NUM_BREAKPOINT_INTERCHROM_OVERLAPS_LONG_NAME
    )
    public int numBreakpointOverlapsInterchrom = 1;
}