Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.sra | |
htsjdk.samtools.util |
Modifier and Type | Method and Description |
---|---|
static Cigar |
TextCigarCodec.decode(java.lang.String textCigar)
Convert from String CIGAR representation to Cigar class representation.
|
Cigar |
SAMRecord.getCigar()
Do not modify the value returned by this method.
|
Cigar |
BAMRecord.getCigar() |
static Cigar |
SAMUtils.getMateCigar(SAMRecord rec)
Returns the Mate Cigar or null if there is none.
|
static Cigar |
SAMUtils.getMateCigar(SAMRecord rec,
boolean withValidation)
Returns the Mate Cigar or null if there is none.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
SAMUtils.cigarMapsNoBasesToRef(Cigar cigar)
Determines if a cigar has any element that both consumes read bases and consumes reference bases
(e.g.
|
static java.lang.String |
TextCigarCodec.encode(Cigar cigar)
Convert from Cigar class representation to String.
|
static java.util.List<AlignmentBlock> |
SAMUtils.getAlignmentBlocks(Cigar cigar,
int alignmentStart,
java.lang.String cigarTypeName)
Given a Cigar, Returns blocks of the sequence that have been aligned directly to the
reference sequence.
|
static int |
SAMUtils.getUnclippedEnd(int alignmentEnd,
Cigar cigar) |
static int |
SAMUtils.getUnclippedStart(int alignmentStart,
Cigar cigar) |
protected void |
SAMRecord.initializeCigar(Cigar cigar)
For setting the Cigar string when BAMRecord has decoded it.
|
void |
SAMRecord.setCigar(Cigar cigar) |
void |
BAMRecord.setCigar(Cigar cigar) |
static java.util.List<SAMValidationError> |
SAMUtils.validateCigar(SAMRecord rec,
Cigar cigar,
java.lang.Integer referenceIndex,
java.util.List<AlignmentBlock> alignmentBlocks,
long recordNumber,
java.lang.String cigarTypeName)
Run all validations of the mate's CIGAR.
|
Modifier and Type | Method and Description |
---|---|
Cigar |
SRALazyRecord.getCigar() |
Modifier and Type | Method and Description |
---|---|
void |
SRALazyRecord.setCigar(Cigar value) |
Modifier and Type | Method and Description |
---|---|
static Cigar |
CigarUtil.addSoftClippedBasesToEndsOfCigar(Cigar cigar,
boolean negativeStrand,
int threePrimeEnd,
int fivePrimeEnd)
Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar.
|
Modifier and Type | Method and Description |
---|---|
static Cigar |
CigarUtil.addSoftClippedBasesToEndsOfCigar(Cigar cigar,
boolean negativeStrand,
int threePrimeEnd,
int fivePrimeEnd)
Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar.
|
static int |
SequenceUtil.countDeletedBases(Cigar cigar) |
static int |
SequenceUtil.countInsertedBases(Cigar cigar) |