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2020-09-15
Merge branch 'master' into feat/anchor-matching
Nicholas Noll
2020-09-15
fix: vectorized entropy computation
Nicholas Noll
2020-09-15
fix: moved to use numpy array instead of slicing AlignIO object
Nicholas Noll
2020-09-10
fix: changed score from average tree branch length to average column entropy ...
Nicholas Noll
2020-09-10
fix: properly deal with precondition for edge repair. now only if block lists...
Nicholas Noll
2020-09-10
fix: proper handling of Z2 flipped orientations
Nicholas Noll
2020-09-10
fix: more consistent handling of left/right extension
Nicholas Noll
2020-09-02
feat: added output of alignments to logging
Nicholas Noll
2020-08-20
fix: small name change v2
Nicholas Noll
2020-08-20
fix: small name change
Nicholas Noll
2020-08-20
fix: allow manual override for tmp directory number
Nicholas Noll
2020-08-20
fix: reharmonize syntax of log file
Nicholas Noll
2020-08-20
fix: harmonize log file syntax
Nicholas Noll
2020-08-20
feat: added prototype for plotting log file data
Nicholas Noll
2020-08-20
fix: pass in cli parameters into union function now
Nicholas Noll
2020-08-20
feat: window and extend for end repair now CLI parameters
Nicholas Noll
2020-08-19
fix: remove new lines from input stream
Nicholas Noll
2020-08-19
fix: use a string buffer
Nicholas Noll
2020-08-19
fix: corrected the iterator
Nicholas Noll
2020-08-19
feat: added simple fasta parser
Nicholas Noll
2020-08-19
chore: update makefile to redirect to correct targets
Nicholas Noll
2020-08-18
fix: added left and right extension back in
Nicholas Noll
2020-08-18
fix: odd bug associated to non-unicode characters in stream
Nicholas Noll
2020-08-18
fix: slicing bug that lead to incorrect lengths
Nicholas Noll
2020-08-18
fix: correctly deal with block offsets when slicing for sequences
Nicholas Noll
2020-08-18
fix: made window offset a global parameter in anticipation of a cli parameter
Nicholas Noll
2020-08-18
feat: use fixed width window into each block for end alignment instead of ent...
Nicholas Noll
2020-08-13
feat: now assess the alignment based on total tree length
Nicholas Noll
2020-08-13
feat: prototype of mafft alignment of blocks
Nicholas Noll
2020-08-13
fix: bug associated to position of using index absolutely instead of relative...
Nicholas Noll
2020-08-13
fix: deal with inverted cases for block lists
Nicholas Noll
2020-08-13
fix: pull out interval of merged blocks and not just the first one
Nicholas Noll
2020-08-12
fix: remove profile import
Nicholas Noll
2020-08-12
fix: remove profiling code
Nicholas Noll
2020-08-11
fix: compute position of each block using path class to ensure its accurate
Nicholas Noll
2020-08-11
fix: circular slicing check for singleton paths
Nicholas Noll
2020-08-11
fix: slicing of sequence paths
Nicholas Noll
2020-08-11
fix: unpack and pack tuple on json serialization for block positions
Nicholas Noll
2020-08-11
feat: blocks now store their position (not modulo length) along the path
Nicholas Noll
2020-07-28
fix: must strip gaps upon sequence extraction to have offset correct
Nicholas Noll
2020-07-28
fix: make try except more localized to not catch all exceptions
Nicholas Noll
2020-07-28
fix: updated improper property accesses
Nicholas Noll
2020-07-28
fix: updated the function calling convention of merge
Nicholas Noll
2020-07-28
proto: implemented first pass at dealing with degenerate chains in the same i...
Nicholas Noll
2020-07-28
feat: added path mergers to deal with transitive edges
Nicholas Noll
2020-07-28
fix: remove non-junctions associated to singleton paths
Nicholas Noll
2020-07-28
fix: correct set of lists
Nicholas Noll
2020-07-28
feat: initial cases for merging implemented as remove_transitives
Nicholas Noll
2020-07-28
feat: added stringifier method to junction for debugging
Nicholas Noll
2020-07-28
fix: small typos
Nicholas Noll
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