public class DuplicateScoringStrategy extends Object
Modifier and Type | Class | Description |
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static class |
DuplicateScoringStrategy.ScoringStrategy |
Constructor | Description |
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DuplicateScoringStrategy() |
Modifier and Type | Method | Description |
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static int |
compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy) |
Compare two records based on their duplicate scores.
|
static int |
compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar) |
Compare two records based on their duplicate scores.
|
static short |
computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy) |
Returns the duplicate score computed from the given fragment.
|
static short |
computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar) |
Returns the duplicate score computed from the given fragment.
|
public static short computeDuplicateScore(SAMRecord record, DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
public static short computeDuplicateScore(SAMRecord record, DuplicateScoringStrategy.ScoringStrategy scoringStrategy, boolean assumeMateCigar)
public static int compare(SAMRecord rec1, SAMRecord rec2, DuplicateScoringStrategy.ScoringStrategy scoringStrategy, boolean assumeMateCigar)
public static int compare(SAMRecord rec1, SAMRecord rec2, DuplicateScoringStrategy.ScoringStrategy scoringStrategy)