Added suffx array and lcp creation test code for Python.
Added SuperMaximumRepeats class, first steps towards a find_blocks
method implementation.
More work on finding the SuperMaximumRepeats of two witnesses.
RangeSet: Switched out RangeSet class from pyrangeset library for
RangeSet class from ClusterShell project. This fixed a TODO in the unit
test.
Added Collation class, Witness class, skeletal VariantGraph class.
Wired Collation, SuperMaximumRepeat and Block class together.
Reorganized classes into core and suffix modules
More work done on the merge method of CollationAlgorithm class.
Build initial block to vertices map.
Added block_to_token map.
More work done on the DekkerSuffixAlgorithm class.
Added darwin integration test to python port.
Added code to output dot files for testcases.
Calculate the Burrows and Wheelers transform from the SA.
Added calculation of LCP array intervals.
Abandoned (super) maximal repeats approach and started new method for
finding non overlapping repeating blocks based on LCP array.
More work on get_non_overlapping_repeating_blocks() method. Unit tests
with two and three witnesses work now.
VariantGraph: changed vertex creation to deal with the fact that the
contents of a token is not unique. Also makes the dot output more alike
the Java one.
Added BlockWitness, Occurrence classes. Added get_first_block_witness
method on Collation class.
Added get_lcp_intervals() method to Collation class.