- getSAMFileSamples
Pull out the samples from a SAMFileHeader; note that we use a TreeSet so that
they are sorted
- createRandomRead
- sortReadsByCoordinate
Returns the collections of reads sorted in coordinate order, according to the
order defined in the r
- getBasesReverseComplement
Returns the reverse complement of the read bases
- hasWellDefinedFragmentSize
Can the adaptor sequence of read be reliably removed from the read based on the
alignment of read an
- convertReadQualToString
Given a read, outputs the base qualities in a string format
- getAdaptorBoundary
Finds the adaptor boundary around the read and returns the first base inside the
adaptor that is clo
- getFirstInsertionOffset
If a read starts in INSERTION, returns the first element length. Warning: If the
read has Hard or So
- getLastInsertionOffset
If a read ends in INSERTION, returns the last element length. Warning: If the
read has Hard or Soft
- getReadCoordinateForReferenceCoordinate
Pre-processes the results of
getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int) to take car
- getReadCoordinateForReferenceCoordinateUpToEndOfRead
- isInsideRead
Is a base inside a read?