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Created with Raphaël 2.2.028Nov20191824Oct18713Sep114229Aug222023Jul1213Jun126329May2824222117151324Apr2322181210843222Mar2113121185429Feb282321201915128526Jan25242218121110947Dec5410Nov76331Oct3026242320161210654225Jul208Jun26May252217521Apr20TEST add cimoved functions into the class as methods; added a few attributesfinished sorting the functions in several filesemptied this file by putting the functions in other filesrenamed filecontinued code refactoring. removed global variable segments_on_target_genome, sorted functions in several filesattempt to reorganize the python fileslimited imports between filessplit functions from Graph_gff in two files, load_intersect and graph_annotadded option to not output duplicated features in annotation, only the best occurence is kept. corrected the alignment option, it now doesnt print features that didnt pass the filters.added new version for benchmarkload intersect is now much quicker. however there might be unexpected behaviour in detect_gene_copies (or maybe elsewhere) if a segment is present several times in a feature (duplication within the feature). this case was not encountered in rice and human data, but it is technically possible.Merge branch 'main' of forge.ird.fr:diade/dynadiv/grannotdelete the intersect file after loading it, it takes too much spaceAdding good licenceReplace LICENSE for GNU GPLv3debug haplotype output. it used to output the haplotype transfer for each walk (chr/ctg).modified how the feature ids are used to handle features fragmented on several lines in the gffadded a check that the sourge and target genome names are found in the walks/paths of the graphchanged how Segments are stored while loading the intersect. now can handle duplicate segments in the source genome (it used to cause negative positions in var output)added header to var outputremoved debug printcommented debug print linesfixed haplotype option, it didnt work when -sh was absentchanged the id of the segments to remove the sspell checkadded error message when the intersect is emptyspecified input data formatadd installation methodremoved warning from bedtoolsmoved filesmoved filesgenerated new dist files with the bug fixbug fix for the PAV matrix output1.0.31.0.3bug fix, grannot now accepts graphs where some chromosomes are split on several walksadded tqdm in dependenciesrenammed dist filesupdate package distribution filesorganised arguments in groups; set conditions for some arguments1.0.21.0.2corrected requirements for option -pav