Speed up (#577)

* use Bio::SeqFeature::Lite

* use SeqFeature::Lite and replace frame by phase

* remove TempDir::Tiny Scalar::Util and Storable

* replace 1 by . in frame fr source feature

* remove perl-storable not used anymore

* clean _gff3_string and update escape_gff3 and unescape_gff3 function for efficiency

* move pipeline

* add devcontainer

* add package AGAT::BatchedGFFWriter, and use the write_feature of this package allowing to send feature by batch and gain more than  40% writing time

* update for HPC

* deal with gz

* set proper version

* get rid of IPC::ShareLite to avoid race condition

* remove IPC::ShareLite

* use tmp file for progress bar

* fix #583

* fix #585

backup to avoid race condition crash, thrrow a warning instead

reactivate progress bar for cpu 0

fix #550 (#551)

* use check_level1_position instead of check_gene_position

* increment version

* improve check level1/level2 position and #fix 550

* add a test for agat_sp_keep_longest_isoform

* fix test due to fix #550

avoid warning Use of uninitialized value in case ouID created becaus… (…

…#548)

* avoid warning Use of uninitialized value  in case ouID created because no ID in the original feature

* suppress annoying Use of uninitialized value

* generalize the script, allow to move up or/and down

* add Devel::Cover

* add previous version of dependency

* add previous version of dependency

* add comment

fix #457 remove attribute in gene_id and transcript_id to keep only t…

…he first … (#496)

* remove multi values in special attributes gene_id and transcript_id to keep only the first one. The others are saved in agat_other_gene_id or agat_other_ transcript_id

* when using merge_overlap_loci avoid to merge value for ID Parent and no gene_id too. Avoid to add ID created on the fly when creating merged_.

* add a deflate_attribute parameter. Make also a global variable for CONFIG to be available from everywhere (filled by get_agat_config)

* Update and add tests

Clean l1 (#491)

* remove transcript ID in Level1 feature when creating it from another feature used as template (clean_clone)
* fix test to reflect that transcript_id not part of level1

Update AGAT.pm

Fix 445 buggit add lib/AGAT/OmniscientI.pm Few gene in output due to… (…

…#447)

* Fix 445 bug introduced in version 1.3.2 in lib/AGAT/OmniscientI.pm : Few gene in output due to a remaining last that quit early in a loop.  remove useless print

* increment version

fix #441 use L3 feature instead to L1 as template to create features …

…when transcript_id exists (#442)

* use L3  feature as template instead of L1 to be able to use proper transcript_id when converting to GTF

* when using clean_clone with clean_attributes, remove Parent and transcript_id attributes anyway when it is a level1 feature

* adapt tests and add test for issue 441

*  Optimize first test in "_check_l2_linked_to_l3" to see if an L1 feature already exists (check among all tags)