Package | Description |
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htsjdk.samtools |
Modifier and Type | Method and Description |
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java.util.List<AlignmentBlock> |
SAMRecord.getAlignmentBlocks()
Returns blocks of the read sequence that have been aligned directly to the
reference sequence.
|
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 java.util.List<AlignmentBlock> |
SAMUtils.getMateAlignmentBlocks(SAMRecord rec) |
Modifier and Type | Method and Description |
---|---|
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.
|