public class SAMRecordDuplicateComparator extends Object implements SAMRecordComparator, Serializable
Constructor and Description |
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SAMRecordDuplicateComparator() |
SAMRecordDuplicateComparator(List<SAMFileHeader> headers) |
Modifier and Type | Method and Description |
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int |
compare(SAMRecord samRecord1,
SAMRecord samRecord2)
Most stringent comparison.
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int |
duplicateSetCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary.
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int |
fileOrderCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.
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void |
setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
comparing, comparing, comparingDouble, comparingInt, comparingLong, equals, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong
public SAMRecordDuplicateComparator()
public SAMRecordDuplicateComparator(List<SAMFileHeader> headers)
public void setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
public int compare(SAMRecord samRecord1, SAMRecord samRecord2)
compare
in interface Comparator<SAMRecord>
public int duplicateSetCompare(SAMRecord samRecord1, SAMRecord samRecord2)
public int fileOrderCompare(SAMRecord samRecord1, SAMRecord samRecord2)
fileOrderCompare
in interface SAMRecordComparator