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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
2020-08-20feat: added prototype for plotting log file dataNicholas Noll
2020-08-20fix: pass in cli parameters into union function nowNicholas Noll
2020-08-20feat: window and extend for end repair now CLI parametersNicholas Noll
2020-08-19chore: update makefile to redirect to correct targetsNicholas 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: pull out interval of merged blocks and not just the first oneNicholas Noll
2020-07-28feat: added stringifier method to junction for debuggingNicholas Noll
2020-07-27chore: remove last tryprint referenceNicholas Noll
2020-07-27chore: remove cherry filteringNicholas Noll
2020-07-20feat: added script to align extended bases around minimap junctionsNicholas Noll
2020-07-14Merge branch 'master' of https://github.com/nnoll/pangraphNicholas Noll
2020-07-14fix: removed None return if we hit the end of MAXSELFMAPSNicholas Noll
2020-07-13Merge branch 'master' of github.com:nnoll/pangraph into mainNicholas Noll
2020-07-13fix: small changesNicholas Noll
2020-07-13fix: escaped shell commandnnoll
2020-07-13feat: added staph recipe to makefileNicholas Noll
2020-07-13fix: correctly deal with multiple gzipped files by concatenatingNicholas Noll
2020-07-11fix: simplified the plot of figure 1Nicholas Noll
2020-07-11fix: updated makefile to include figure 1 recipeNicholas Noll
2020-07-11feat: prototype of figure 1 pipelineNicholas Noll
2020-07-10feat: added simple cli option to output pangraph json as a fasta of all blocksNicholas 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: changed cut energy to be intensive by default with an optional flag to ...Nicholas Noll
2020-07-09feat: assess_algo now iterates through the different generated pangraph. stor...Nicholas Noll
2020-07-08feat: makefile now generates many different pangraphs as a function of mu and...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
2020-06-30chore: child -> childrenNicholas Noll
2020-06-28feat: makefile now automatically produces algorithm statisiticsNicholas Noll
2020-06-28chore: small changes. more explanation in READMENicholas Noll
2020-06-28feat: added in build step to makefile. added cutoff block length to cliNicholas Noll
2020-06-27many small fixesNicholas Noll
2020-06-15fix: various runtime errors squashedNicholas Noll
2020-06-15feat: makefile now generates variable synthetic dataNicholas Noll
2020-06-15feat: new pipeline from simulation->clustering now worksNicholas Noll
2020-06-15feat: begun prototype for pipelineNicholas Noll
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