56 lines
1.5 KiB
Java
Executable File
56 lines
1.5 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.traversals;
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import net.sf.picard.filter.SamRecordFilter;
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import java.util.Map;
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import java.util.HashMap;
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import org.broadinstitute.sting.utils.Utils;
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/**
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* Created by IntelliJ IDEA.
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* User: hanna
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* Date: Apr 8, 2009
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* Time: 4:13:40 PM
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*
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* Holds a bunch of basic information about the traversal.
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* TODO: Make this a class that can be passed around from the TraversalEngine to other entries that want to update it.
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*/
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public class TraversalStatistics {
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// Number of records (loci, reads) we've processed
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public static long nRecords;
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// How many reads have we processed, along with those skipped for various reasons
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public static long nReads;
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public static long nSkippedReads;
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public static long nUnmappedReads;
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public static long nNotPrimary;
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public static long nBadAlignments;
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public static long nSkippedIndels;
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public static long nDuplicates;
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public static Map<Class, Long> counter = new HashMap<Class, Long>();
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static {
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reset();
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}
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public static void incrementFilter(SamRecordFilter filter) {
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long c = 0;
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if ( counter.containsKey(filter.getClass()) ) {
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c = counter.get(filter.getClass());
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}
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counter.put(filter.getClass(), c + 1L);
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}
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public static void reset() {
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nRecords = 0;
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nReads = 0;
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nSkippedReads = 0;
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nUnmappedReads = 0;
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nNotPrimary = 0;
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nBadAlignments = 0;
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nSkippedIndels = 0;
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nDuplicates = 0;
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}
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}
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