Package | Description |
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htsjdk.samtools |
Modifier and Type | Method and Description |
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static SamPairUtil.PairOrientation |
SamPairUtil.getPairOrientation(SAMRecord r)
Computes the pair orientation of the given SAMRecord.
|
static SamPairUtil.PairOrientation |
SamPairUtil.PairOrientation.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static SamPairUtil.PairOrientation[] |
SamPairUtil.PairOrientation.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
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static boolean |
SamPairUtil.isProperPair(SAMRecord firstEnd,
SAMRecord secondEnd,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations) |
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> exepectedOrientations)
This method will clear any mate cigar already present.
|
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> exepectedOrientations,
boolean addMateCigar) |
static void |
SamPairUtil.setProperPairFlags(SAMRecord rec1,
SAMRecord rec2,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations) |