NBISweden / AGAT / 20279205314
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coverage: 69.178% (-12.0%) from 81.2%
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Parallel version of AGAT (#549)

* fix #507 - add option raw to print raw data in a dedidcated folder

* clean indentation

* first draft to parallelizing

* add paramas part1

* change threads to cpu

* parallel param set

* add cpu in help and in agat e

* e,nd

* good job, I'm on the way

* add same update as v1.5.0

* indentation

* adapt to remove the use of mRNAGeneLink

* replace external mRNAGeneLink into an l2tol1 hash internal to omniscient

* add function to clean test outputs

* fix conflict2

* update version

* add issue457 test

* remove Parent from level1 to avoid bbad interpreation

* remove duplicate option

* improve cleaning output

* improve cleaning output

* improve cleaning

* parallel ok

* fix dry mode when merging

* working parallel version

* improve print_omniscient_keys

* peafine

* set l2tol1 and hashID aside in omniscient in other hash. Allow use ancient parsing way without forking using cpu to 0

* clean log STDOUT

* fix indentation and add use IPC::Shareable

* add +minimum_chunk_size:

* fix call to remove config

* update Bio::SeqFeature::Generic call for performance improvement

* improve and add cache

* try to use cache

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* add make

* remove a useless export

* remove test for undef because can now exists in hasID

* fix test

* replace IPC::Shareable by IPC::ShareLite to be able to install via conda

* add IPC::ShareLite and remove IPC::Shareable and IPC::Open2

* Pipe-safe scripts and refactored tests, and unified CLI options inspired by #559 from @kim-fehl and more

* try debug a sorting error

* short

* Force a deterministic locale for sorting/compare

* set ubuntu 24.04

* add convenient way to update the end of each script pod

* add possibility to read gz compressed files to all sq files. Update/add progress bar to sq files. standardise POD. Fix hel... (continued)

13886 of 20073 relevant lines covered (69.18%)

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ID Job ID Ran Files Coverage
1 20279205314.1 113
69.18
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Source Files on build 20279205314