fix NBISweden#457 remove attribute in gene_id and transcript_id to ke…

…ep only the first … (NBISweden#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 (NBISweden#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… (…

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

…features when transcript_id exists (NBISweden#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)

add parameter to clean Name,product,dbxref,product attributes. Append… (

NBISweden#438)

* add parameter to clean Name,product,dbxref,product attributes. Append and do not replace attribute by default. Avoid pathway when it is - because endup in the DBxref attribute + update doc + adapt test with clean_name parameter

Update doc (NBISweden#432)

*  Update README.md and add term-progressbar in the list of dependencies (forgotten long time ago). 
* Add a dockerfile to make image with all needed dependencies to install AGAT

set version to v1.2.0

Fix NBISweden#352 - do not check feature when already removed (NBISwe…

…den#355)

Co-authored-by: Jacques Dainat <[email protected]>

Update README.md