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AGAT-v0.2.0
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@Juke34 Juke34 released this 10 Mar 20:36
· 393 commits to master since this release
v0.2.0
7a3a915
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Learn about vigilant mode.

Fixes:
#22 update printSurrounded to avoid line truncation
#23 agat_sq_basic_statistics.pl, add parameter to inflate multi-parent features
#24 agat_sp_extract_sequences.pl, now deals with seq < 3 nucleotide or empty translation
#25 update message in agat_sp_merge_annotations.pl
#27 add converter agat_convert_genscan2gff.pl

New scripts:
agat_convert_sp_gff2gtf.pl
agat_convert_sp_gxf_to_gxf.pl (copy of agat_sp_gxf_to_gff3.pl)
agat_convert_embl2gff.pl
agat_convert_mfannot2gff.pl
agat_convert_sp_gff2bed.pl
agat_sp_kraken_assess_lift_coverage.pl
agat_convert_genscan2gff.pl

Updates:
update features_level.json to handle more ensembl feature types

  • esthetic changes
    fix STDOUT for agat_sp_filter_feature_by_attribute_presence.pl
    fix CDS starting offset in agat_sp_extract_sequences (translation in protein was wrong if starting CDS phase was different than 0. We clip now 1 or 2 nucleotide when needed to start in the correct frame)
    add test for the new scripts
    update OmniscienI to deal with no_check_skip option as an array + lower case key in uniqID hash + deal differently in _check_l2_linked_to_l3 to better create l2 feature (update gff_syntax test case9 to reflect the change).
    ...
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