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2020-09-15fix: moved to use numpy array instead of slicing AlignIO objectNicholas 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: reharmonize syntax of log fileNicholas Noll
2020-08-20fix: small typosNicholas Noll
2020-08-20feat: added prototype for plotting log file dataNicholas 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
2020-07-27chore: add ylimNicholas Noll
2020-07-27fix: added length filterNicholas Noll
2020-07-27chore: checkinNicholas Noll
2020-07-27fix: manually reverse_complementNicholas Noll
2020-07-27fix: updated assay_junctions to correctly deal with inverted alignmentsNicholas Noll
2020-07-23chore: change bandwidthNicholas Noll
2020-07-23feat: can now scan alignment by bandwidthNicholas Noll
2020-07-22chore: move from pyopa to seqanpyNicholas Noll
2020-07-22fix: forgot to finish renameNicholas Noll
2020-07-20feat: log how many blocks are contained in extension zoneNicholas Noll
2020-07-20feat: added script to align extended bases around minimap junctionsNicholas Noll
2020-07-11feat: added cli flag to build that will output statistics on all intermediate...Nicholas Noll
2020-07-11fix: simplified the plot of figure 1Nicholas Noll
2020-07-11chore: add seabornNicholas Noll
2020-07-11feat: prototype of figure 1 pipelineNicholas Noll
2020-07-09fix: dates are now computed correctly for each block and only onceNicholas Noll
2020-07-09chore: increase population size for simulationNicholas Noll
2020-07-09feat: assess_algo now iterates through the different generated pangraph. stor...Nicholas Noll
2020-07-08fix: started initial fixes for assess_algo to iterate over all mu and beta va...Nicholas Noll
2020-07-08feat: pangraph build now outputs graph to stdoutNicholas Noll
2020-07-08fix: changed coverage to report the dates of all breakpoints instead of just ...Nicholas Noll
2020-07-08fix: mode doesn't return countsNicholas Noll
2020-07-08feat: coverage now returns the found blocks and their associated timesNicholas Noll
2020-07-08fix: assay_algo now deals with no match case properlyNicholas Noll
2020-07-08feat: added length of each hitNicholas Noll
2020-07-08fix: accuracy (distance displaced) now correctly deals with composite blocksNicholas Noll
2020-07-08fix: allowed for composite matches to ancestral tilesNicholas Noll
2020-06-28feat: makefile now automatically produces algorithm statisiticsNicholas Noll
2020-06-28fix: removed unneeded map and moved to list comprehensionNicholas Noll
2020-06-28feat: added match coverage and breakpoint difference computation to algorithm...Nicholas Noll
2020-06-28feat: added skeleton for the algorithm assessment with synthetic dataNicholas Noll
2020-03-08chore: removed old scripts from packageNicholas Noll
2020-03-08beginning restructuring of codeNicholas Noll
2019-12-11loose file to commitNicholas Noll
2019-12-10commiting commentsNicholas Noll
2019-12-02updatedNicholas Noll
2019-11-04changedNicholas Noll
2019-11-04changedNicholas Noll
2019-10-19suffix tree prototypeNicholas Noll
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