- May 21, 2024
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nina.marthe_ird.fr authored
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- May 17, 2024
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nina.marthe_ird.fr authored
adapted the multicopies code to the output of -var. corrected the positions in the output gff for the inversions
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- May 15, 2024
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nina.marthe_ird.fr authored
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- May 13, 2024
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nina.marthe_ird.fr authored
added gene multicopies handling. new function detect_copies, and now the target_genome_path of child features and the transfer depend on the parent feature
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- Apr 24, 2024
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nina.marthe_ird.fr authored
changed how the features are transfered. now after the transfer of a gene, all its child features are transfered with it. this automatically sorts the output gff, and makes easier the handling of the cov and id filters (if a gene didnt pass, dont transfer its chids, etc)
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- Apr 23, 2024
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nina.marthe_ird.fr authored
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- Apr 22, 2024
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nina.marthe_ird.fr authored
now always use the function get_seg_occ to get the right segment occurence. so now the option -ann outputs the target genome gff with all the copies of the genes if -cov and -id are at 0
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- Apr 18, 2024
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nina.marthe_ird.fr authored
added a function to get the right segment occurence, given the segment_id,walk_name,feature_id,copy_id
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nina.marthe_ird.fr authored
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- Apr 12, 2024
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nina.marthe_ird.fr authored
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- Apr 10, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
modified how the feature paths in the target genomes are found; now several can be found, on several walks (chr/ctg); adapted how the features are transfered (only for the genome annotation transfer, not for the graph_gaf/gff, variations and alignment)
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- Apr 08, 2024
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nina.marthe_ird.fr authored
the dict segments_on_target_genome now stores the segment twice if it is present twice in a given walk. adapted the rest of the code to use the last occurence (like before, will change that later)
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- Apr 02, 2024
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nina.marthe_ird.fr authored
inverted the start and stop positions in the output gff when the stop was before the start (in inverted regions)
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- Mar 22, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
the function that generates the target genomes gff now doesnt transfer if the coverage or id is too low
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- Mar 21, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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- Mar 13, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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- Mar 12, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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- Mar 11, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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- Mar 08, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
adapted to keep the orientation of the segments from the walks. added functions to better handle inversions
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- Mar 05, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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- Mar 04, 2024
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nina.marthe_ird.fr authored
adapted the code to use the options for the output files. changed every instance of 'clustal' to 'aln' in the code
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- Feb 21, 2024
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nina.marthe_ird.fr authored
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- Feb 20, 2024
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nina.marthe_ird.fr authored
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- Feb 19, 2024
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nina.marthe_ird.fr authored
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nina.marthe_ird.fr authored
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