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/*
* The MIT License
*
* Copyright (c) 2009 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;
import java.io.Serializable;
/**
* Comparator for sorting SAMRecords by coordinate. Note that the header is required because
* the order of sequences in the header defines the major sort order.
*
* Ideally this method would only return 0 for completely equal SAMRecords, so that sort is
* completely deterministic. This implementation does not achieve this completely, but it
* comes pretty close, while avoiding decoding the variable length fields, except for read name,
* which is decoded if coordinate and strand are equal.
*
* Extreme care must be taken to ensure the following:
* if A == B, then B == A
* if A < B, then B > A
* if A < B && B < C, then A < C
*
*/
public class SAMRecordCoordinateComparator implements SAMRecordComparator, Serializable {
private static final long serialVersionUID = 1L;
@Override
public int compare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
int cmp = fileOrderCompare(samRecord1, samRecord2);
if (cmp != 0) {
return cmp;
}
// Test of negative strand flag is not really necessary, because it is tested
// with cmp if getFlags, but it is left here because that is the way it was done
// in the past.
if (samRecord1.getReadNegativeStrandFlag() == samRecord2.getReadNegativeStrandFlag()) {
cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName());
if (cmp != 0) return cmp;
cmp = compareInts(samRecord1.getFlags(), samRecord2.getFlags());
if (cmp != 0) return cmp;
cmp = compareInts(samRecord1.getMappingQuality(), samRecord2.getMappingQuality());
if (cmp != 0) return cmp;
cmp = compareInts(samRecord1.getMateReferenceIndex(), samRecord2.getMateReferenceIndex());
if (cmp != 0) return cmp;
cmp = compareInts(samRecord1.getMateAlignmentStart(), samRecord2.getMateAlignmentStart());
if (cmp != 0) return cmp;
cmp = compareInts(samRecord1.getInferredInsertSize(), samRecord2.getInferredInsertSize());
return cmp;
}
else return (samRecord1.getReadNegativeStrandFlag()? 1: -1);
}
private int compareInts(int i1, int i2) {
if (i1 < i2) return -1;
else if (i1 > i2) return 1;
else return 0;
}
/**
* Less stringent compare method than the regular compare. If the two records
* are equal enough that their ordering in a sorted SAM file would be arbitrary,
* this method returns 0. If read is paired and unmapped, use the mate mapping to sort.
* Records being compared must have non-null SAMFileHeaders.
*
* @return negative if samRecord1 < samRecord2, 0 if equal, else positive
*/
@Override
public int fileOrderCompare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
if (null == samRecord1.getHeader() || null == samRecord2.getHeader()) {
throw new IllegalArgumentException("Records must have non-null SAMFileHeaders to be compared");
}
final int refIndex1 = samRecord1.getReferenceIndex();
final int refIndex2 = samRecord2.getReferenceIndex();
if (refIndex1 == -1) {
return (refIndex2 == -1? 0: 1);
} else if (refIndex2 == -1) {
return -1;
}
final int cmp = refIndex1 - refIndex2;
if (cmp != 0) {
return cmp;
}
return samRecord1.getAlignmentStart() - samRecord2.getAlignmentStart();
}
}
