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Created with Raphaël 2.2.03Mar26Feb30Jan2924211528Nov20191824Oct18713Sep114229Aug222023Jul1213Jun126329May2824222117151324Apr2322181210843222Mar2113121185429Feb282321201915128526Jan25242218121110947Dec5410Nov76331Oct3026242320161210654225Jul208Jun26May252217521Apr20modified how the parent field is detected in gff, made it more flexibleturn feature path list into set to check faster if seg is present, in var detail and aln; ignore case where a segment is twice in a feature pathadded dataverse linkremoved yates continuity correctionadded scripts for publicationadded the feature strand in target genome in variation details output fileruntime opti, changed feature_seg_list in dictionnary to check if seg present in list, to compute child features paths and to compute cov/id; much faster on human data, not so much on rice and ecoli datafix bug when there are several haplotypes and option -ht is used; didnt fix bug when there are several haplotypes but option -ht is absent, todo add a warningMerge branch 'refactoring'improved how paths and walks are detected and how bed files are attributed to genomes; fixes bug when a genome name was included in another genome namebug fix when a segment is present in both orientation in the source features; modified search_segment to find the orientation that corresponds to the current featurecorrected feature info print in class Featurebug fix; with several chromosomes the features were transfered only on the last one loadedremove buggy releaseMerge branch '3-add-ci' into 'main'4-add-test-ci4-add-test-ciUpdate .gitlab-ci.yml file -TESTUpdate .gitlab-ci.yml file -TEST-TEST-TESTTEST 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 output