5529694815
57%

Ran 12 Jul 2023 09:27AM UTC

Jobs 1

Files 73

Run time 2s

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Build # 5529694815

Build Type

push

github

Committed by

web-flow

Commit Message

Input / output _sq_ _sp_ homogenized (#379)

* fix #378 input auto detection fix for all _sq_ script (param gff_output_version wasted instead of force_gff_input_version)

* add test for agat_sq_add_attributes_from_tsv

* homogenize input/ouput
    - use exclusively AGAT::BioperlGFF (_sq_script was using Bio::Tools::GFF for inout/output;  _sp_ script were using AGAT::BioperlGFF  for input and  Bio::Tools::GFF for output)
    - improving BioperlGFF to take care of GFF and GTF output (adding parameter VERSION and TYPE).  Remind BioperlGFF is an improved version of Bio::Tools::GFF
    - simplify code by factorizing OmniscientToGTF.pm and BioperlGFF.pm by implementing redundant function into BioperlGFF (e.g. filtering feature by GTF version; _gff25_string_JD and _gff25_string to fix incorrect GTF output provided by bioperl, etc) 

Fix doc:
* remove 0 from agar config file which is not a correct to select for GTF version
* remove agat_sq_manage_ID from doc (official script is agat_sq_manage_IDs)

Run Details

11729 of 14551 relevant lines covered (80.61%)

2147.57 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	5529694815.1	12 Jul 2023 09:27AM UTC	73	80.61	GitHub Action Run

NBISweden / AGAT / 5529694815
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