/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
/**
* This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
* during duplicate marking (see MarkDuplicates).
* @author nhomer
*/
public class DuplicateScoringStrategy {
public enum ScoringStrategy {
SUM_OF_BASE_QUALITIES,
TOTAL_MAPPED_REFERENCE_LENGTH
}
/** Calculates a score for the read which is the sum of scores over Q15. */
private static short getSumOfBaseQualities(final SAMRecord rec) {
short score = 0;
for (final byte b : rec.getBaseQualities()) {
if (b >= 15) score += b;
}
return score;
}
/**
* Returns the duplicate score computed from the given fragment.
*/
public static short computeDuplicateScore(final SAMRecord record, final ScoringStrategy scoringStrategy) {
return computeDuplicateScore(record, scoringStrategy, false);
}
/**
* Returns the duplicate score computed from the given fragment.
*
* If true is given to assumeMateCigar, then any score that can use the mate cigar to compute the mate's score will return the score
* computed on both ends.
*/
public static short computeDuplicateScore(final SAMRecord record, final ScoringStrategy scoringStrategy, final boolean assumeMateCigar) {
short score = 0;
switch (scoringStrategy) {
case SUM_OF_BASE_QUALITIES:
score += getSumOfBaseQualities(record);
break;
case TOTAL_MAPPED_REFERENCE_LENGTH:
if (!record.getReadUnmappedFlag()) {
score += record.getCigar().getReferenceLength();
}
if (assumeMateCigar && record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
score += SAMUtils.getMateCigar(record).getReferenceLength();
}
break;
}
return score;
}
/**
* Compare two records based on their duplicate scores. If the scores are equal, we break ties based on mapping quality
* (added to the mate's mapping quality if paired and mapped), then library/read name.
*
* If true is given to assumeMateCigar, then any score that can use the mate cigar to to compute the mate's score will return the score
* computed on both ends.
*
* We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
*/
public static int compare(final SAMRecord rec1, final SAMRecord rec2, final ScoringStrategy scoringStrategy, final boolean assumeMateCigar) {
int cmp;
// always prefer paired over non-paired
if (rec1.getReadPairedFlag() != rec2.getReadPairedFlag()) return rec1.getReadPairedFlag() ? 1 : -1;
cmp = computeDuplicateScore(rec2, scoringStrategy, assumeMateCigar) - computeDuplicateScore(rec1, scoringStrategy, assumeMateCigar);
/**
* Finally, use library ID and read name
* This is important because we cannot control the order in which reads appear for reads that are comparable up to now (i.e. cmp == 0). We want to deterministically
* choose them, and so we need this.
*/
if (0 == cmp) cmp = SAMUtils.getCanonicalRecordName(rec1).compareTo(SAMUtils.getCanonicalRecordName(rec2));
return cmp;
}
/**
* Compare two records based on their duplicate scores. The duplicate scores for each record is assume to be
* pre-computed by computeDuplicateScore and stored in the "DS" tag. If the scores are equal, we break
* ties based on mapping quality (added to the mate's mapping quality if paired and mapped), then library/read name.
*
* We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
*/
public static int compare(final SAMRecord rec1, final SAMRecord rec2, final ScoringStrategy scoringStrategy) {
return compare(rec1, rec2, scoringStrategy, false);
}
}