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2020-09-15Merge pull request #4 from nnoll/feat/anchor-matchingHEADmasterNicholas Noll
2020-09-15Merge branch 'master' into feat/anchor-matchingNicholas Noll
2020-09-15fix: vectorized entropy computationNicholas Noll
2020-09-15fix: moved to use numpy array instead of slicing AlignIO objectNicholas Noll
2020-09-10fix: changed score from average tree branch length to average column entropy ...Nicholas Noll
2020-09-10fix: properly deal with precondition for edge repair. now only if block lists...Nicholas Noll
2020-09-10fix: proper handling of Z2 flipped orientationsNicholas Noll
2020-09-10fix: more consistent handling of left/right extensionNicholas Noll
2020-09-02feat: added output of alignments to loggingNicholas Noll
2020-08-20fix: small name change v2Nicholas Noll
2020-08-20fix: small name changeNicholas Noll
2020-08-20fix: allow manual override for tmp directory numberNicholas Noll
2020-08-20fix: reharmonize syntax of log fileNicholas Noll
2020-08-20fix: harmonize log file syntaxNicholas Noll
2020-08-20fix: small typosNicholas Noll
2020-08-20feat: added prototype for plotting log file dataNicholas Noll
2020-08-20Merge branch 'feat/fasta-parser' into feat/anchor-matchingNicholas Noll
2020-08-20fix: pass in cli parameters into union function nowNicholas Noll
2020-08-20Merge pull request #5 from nnoll/feat/fasta-parserNicholas Noll
2020-08-20feat: window and extend for end repair now CLI parametersNicholas Noll
2020-08-19feat: allow for plasmids and chromosome filteringNicholas Noll
2020-08-19fix: typo in function callNicholas Noll
2020-08-19feat: filter plasmids now works on the directory levelNicholas Noll
2020-08-19fix: remove new lines from input streamNicholas Noll
2020-08-19feat: added code to filter plasmids from chromosomesNicholas Noll
2020-08-19fix: use a string bufferNicholas Noll
2020-08-19fix: corrected the iteratorNicholas Noll
2020-08-19feat: added simple fasta parserNicholas Noll
2020-08-19chore: update makefile to redirect to correct targetsNicholas Noll
2020-08-18fix: added left and right extension back inNicholas Noll
2020-08-18fix: odd bug associated to non-unicode characters in streamNicholas Noll
2020-08-18fix: slicing bug that lead to incorrect lengthsNicholas Noll
2020-08-18fix: correctly deal with block offsets when slicing for sequencesNicholas Noll
2020-08-18fix: made window offset a global parameter in anticipation of a cli parameterNicholas Noll
2020-08-18feat: use fixed width window into each block for end alignment instead of ent...Nicholas Noll
2020-08-13feat: now assess the alignment based on total tree lengthNicholas Noll
2020-08-13feat: prototype of mafft alignment of blocksNicholas Noll
2020-08-13fix: bug associated to position of using index absolutely instead of relative...Nicholas Noll
2020-08-13fix: deal with inverted cases for block listsNicholas Noll
2020-08-13fix: pull out interval of merged blocks and not just the first oneNicholas Noll
2020-08-12Merge pull request #3 from nnoll/feat/merge-transitivesNicholas Noll
2020-08-12fix: remove profile importNicholas Noll
2020-08-12fix: remove profiling codeNicholas Noll
2020-08-11fix: compute position of each block using path class to ensure its accurateNicholas Noll
2020-08-11fix: circular slicing check for singleton pathsNicholas Noll
2020-08-11fix: slicing of sequence pathsNicholas Noll
2020-08-11fix: unpack and pack tuple on json serialization for block positionsNicholas Noll
2020-08-11feat: blocks now store their position (not modulo length) along the pathNicholas Noll
2020-07-28fix: must strip gaps upon sequence extraction to have offset correctNicholas Noll
2020-07-28fix: make try except more localized to not catch all exceptionsNicholas Noll
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