Package | Description |
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htsjdk.samtools |
Modifier and Type | Field and Description |
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static DuplicateScoringStrategy.ScoringStrategy |
SAMRecordSetBuilder.DEFAULT_DUPLICATE_SCORING_STRATEGY |
Modifier and Type | Method and Description |
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static DuplicateScoringStrategy.ScoringStrategy |
DuplicateScoringStrategy.ScoringStrategy.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static DuplicateScoringStrategy.ScoringStrategy[] |
DuplicateScoringStrategy.ScoringStrategy.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
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static int |
DuplicateScoringStrategy.compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
Compare two records based on their duplicate scores.
|
static int |
DuplicateScoringStrategy.compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar)
Compare two records based on their duplicate scores.
|
static short |
DuplicateScoringStrategy.computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
Returns the duplicate score computed from the given fragment.
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static short |
DuplicateScoringStrategy.computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar)
Returns the duplicate score computed from the given fragment.
|
void |
SAMRecordDuplicateComparator.setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy) |
void |
DuplicateSetIterator.setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
Deprecated.
|
Constructor and Description |
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SAMRecordSetBuilder(boolean sortForMe,
SAMFileHeader.SortOrder sortOrder,
boolean addReadGroup,
int defaultChromosomeLength,
DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy) |