Package htsjdk.samtools

Class DuplicateScoringStrategy

java.lang.Object

htsjdk.samtools.DuplicateScoringStrategy

public class DuplicateScoringStrategy
extends Object

This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates).

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	DuplicateScoringStrategy.ScoringStrategy

Constructor Summary

Constructors

Constructor	Description
DuplicateScoringStrategy()

Method Summary

Modifier and Type	Method	Description
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

DuplicateScoringStrategy

public DuplicateScoringStrategy()

Method Details

computeDuplicateScore

public static short computeDuplicateScore(SAMRecord record,
 DuplicateScoringStrategy.ScoringStrategy scoringStrategy)

Returns the duplicate score computed from the given fragment.

computeDuplicateScore

public static short computeDuplicateScore(SAMRecord record,
 DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
 boolean assumeMateCigar)

Returns the duplicate score computed from the given fragment. value should be capped by Short.MAX_VALUE/2 since the score from two reads will be added and an overflow will be 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.

compare

public static int compare(SAMRecord rec1,
 SAMRecord rec2,
 DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
 boolean assumeMateCigar)

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.

compare

public static int compare(SAMRecord rec1,
 SAMRecord rec2,
 DuplicateScoringStrategy.ScoringStrategy scoringStrategy)

Compare two records based on their duplicate scores. The duplicate scores for each record is assumed 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.