gatk-3.8/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java

package org.broadinstitute.sting.gatk.traversals;

import net.sf.picard.filter.SamRecordFilter;

import java.util.Map;
import java.util.HashMap;

import org.broadinstitute.sting.utils.Utils;

/**
 * Created by IntelliJ IDEA.
 * User: hanna
 * Date: Apr 8, 2009
 * Time: 4:13:40 PM
 *
 * Holds a bunch of basic information about the traversal.
 * TODO: Make this a class that can be passed around from the TraversalEngine to other entries that want to update it.
 */
public class TraversalStatistics {
    // Number of records (loci, reads) we've processed
    public static long nRecords;
    // How many reads have we processed, along with those skipped for various reasons
    public static long nReads;
    public static long nSkippedReads;
    public static long nUnmappedReads;
    public static long nNotPrimary;
    public static long nBadAlignments;
    public static long nSkippedIndels;
    public static long nDuplicates;
    public static Map<Class, Long> counter = new HashMap<Class, Long>();

    static {
        reset();
    }

    public static void incrementFilter(SamRecordFilter filter) {
        long c = 0;
        if ( counter.containsKey(filter.getClass()) ) {
            c = counter.get(filter.getClass());
        }

        counter.put(filter.getClass(), c + 1L);
    }

    public static void reset() {
        nRecords = 0;
        nReads = 0;
        nSkippedReads = 0;
        nUnmappedReads = 0;
        nNotPrimary = 0;
        nBadAlignments = 0;
        nSkippedIndels = 0;
        nDuplicates = 0;
    }
}