Instead of storing a flat sequence of AlignmentType operations, the aligner now stores a sequence of AlignmentType operations ("actions") and a sequence of counts which runlength-encode the flat sequence.
Added functions to the AlignmentImpl class to store and obtain the RLE sequences and convert them to a CIGAR string. The class maintains backward compatibility for aligners that still provide the flat sequence. Those aligners need to be adapted in the future.
banded Myers algorithm: Handle special cases, where query length and/or target length are 0.
AlignmentType
operations, the aligner now stores a sequence ofAlignmentType
operations ("actions") and a sequence ofcounts
which runlength-encode the flat sequence.AlignmentImpl
class to store and obtain the RLE sequences and convert them to a CIGAR string. The class maintains backward compatibility for aligners that still provide the flat sequence. Those aligners need to be adapted in the future.