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  • 2270de2ab23868548486d3f4d045aad4b8e8aa63
  • main default protected
  • inferences
  • multiannot
  • syntegroup
  • 1.0.2
  • 1.0.1
  • 1.0.0
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Created with Raphaël 2.2.028Oct922Sep19181229Aug222113116425Jul23181614May12625Apr1817161597331Mar121154326Feb30Jan2924211528Nov20191824Oct18713Sep114229Aug222023Jul1213Jun126329May2824222117151324Apr2322181210843222Mar2113121185429Feb282321201915128526Jan25242218121110947Dec5410Nov76331Oct3026242320161210654225Jul208Jun26May252217521Apr20update species testmainmainfix install bugEdit README.md to include test data, add the citation for the preprint, and add the apptainer def file as an installation methodMerge branch 'main' of forge.ird.fr:diade/dynadiv/grannotadded script to compare inversions between liftoff and grannotupdate time comparison with graph construction timeadd dependencies version in pyproject and readmefixed stat; duplicated features used to inflate the statistics and result in negative number of features transferred; also detected an issue with copies detection, todoUpdated container and pyproject for 24.04, with the help of S RavelAdding first version of Grannot Singularity containeradded header to output files, that inform on what transfer has been performedadded brackets for pvalues on figureschanged names of categories in figurefixed line count in files;adapted path name detection to names without haplotypefix handling of intersect filecorrect header in var filefixed file extension and added header to gffcorrect error message displaymultiannot synt…multiannot syntegrouptried to implement a new method to compare overlaping mrna annotationsadd size attribute to Segment classremove debug printcorrect stat file creationfixed the multiple annotations logs and stats output filescanceled the gene position correction to match the adopted mrna; changed the name of the parent in the annotation for the adopted mrnathe outdir path can now include non-existing directorieschanges the gene start position its first segment if the adopted mrna starts before the gene; still has to treat the case where the adopted mrna starts on a different segmentMerge branch 'multiannot' of forge.ird.fr:diade/dynadiv/grannot into multiannotremove debug printcorrect commentnow even the source genomes are set as target when no target genome is givenbetter printadded print for featurepathsnow the source genomes can also be target genomesadded load bar for overlaps; added prints for overlap processingsplit code for overlap in several files; split code in more functions; color error messagesadded comments for multiannot, and an error message when a feature is incomplete (most likely gff format error)bug fix when no target genome is given by the user; now handles source genome as a list instead of a single stringadded the transfer of adopted mrna on target genomefixed get_adopted_childs from class Featureremove print