NBISweden / AGAT / 24252676901

61%

Build Type

push

github

Committed by web-flow

Commit Message

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

Coverage Stats

109 of 196 new or added lines in 5 files covered. (55.61%)

6 existing lines in 3 files now uncovered.

11364 of 17460 relevant lines covered (65.09%)

265.36 hits per line