Package | Description |
---|---|
htsjdk.samtools |
Modifier and Type | Method and Description |
---|---|
List<AlignmentBlock> |
SAMRecord.getAlignmentBlocks()
Returns blocks of the read sequence that have been aligned directly to the
reference sequence.
|
static List<AlignmentBlock> |
SAMUtils.getAlignmentBlocks(Cigar cigar,
int alignmentStart,
String cigarTypeName)
Given a Cigar, Returns blocks of the sequence that have been aligned directly to the
reference sequence.
|
static List<AlignmentBlock> |
SAMUtils.getMateAlignmentBlocks(SAMRecord rec) |
Modifier and Type | Method and Description |
---|---|
static List<SAMValidationError> |
SAMUtils.validateCigar(SAMRecord rec,
Cigar cigar,
Integer referenceIndex,
List<AlignmentBlock> alignmentBlocks,
long recordNumber,
String cigarTypeName)
Run all validations of the mate's CIGAR.
|