https://github.com/alejandrogzi/gxf2bed - v0.2.6

What's new on 0.2.6

• Solved missing UTRs (@MustafaElshani ) [#9 ]

- Rust
Published by alejandrogzi 10 months ago

https://github.com/alejandrogzi/gxf2bed - v0.2.5

What's new on v0.2.5 - Fixes a bug with child nodes, overwriting coords - Fixes a bug with a wrong delimiter when using gff.gz as inputs - Re-implements the algorithm for a most efficient node tree - Adds additional unit tests

- Rust
Published by alejandrogzi about 1 year ago

https://github.com/alejandrogzi/gxf2bed - v0.2.4

What's new on v0.2.4

• Fixes a bug on cases missing child nodes (see Issue #3)
• Introduces a brief description on how to use --parent/--child/--feature flags in README
• Changes to a faster compression algorithm for .bed.gz

- Rust
Published by alejandrogzi about 1 year ago

https://github.com/alejandrogzi/gxf2bed - v0.2.3

What's new on v.0.2.3

• gxf2bed now is even x2 faster and can convert the human annotation in 1.5 seconds!
• including bench to support results in README and update benchamrk results + metrics.
• implements free compressed conversion between formats: gtf/gtf.gz/gff/gff.gz to bed/bed.gz!

- Rust
Published by alejandrogzi over 1 year ago

https://github.com/alejandrogzi/gxf2bed - v0.2.2

What's new on v.0.2.2

• Allows translation without relationships to be compatible with Prokka outputs
• To perform plain translation without hierarchy just explicitly declare --parent "" --child ""

- Rust
Published by alejandrogzi almost 2 years ago

https://github.com/alejandrogzi/gxf2bed - v0.2.1

What's new on v0.2.1

• Fixes some rare GTF bugs due to extra '\n' at the end (malformed GTFs)
• Adds test modules for record parsing and attr parsing
• Build a nextflow module! Thanks to @edmundmiller!
• Updates run times. Now gxf2bed is faster (~0.7s +/-0.2s) due to a change in the hashing algo (now using hashbrown)!

- Rust
Published by alejandrogzi about 2 years ago

https://github.com/alejandrogzi/gxf2bed - v0.2.0

What's new on v.0.2

• Now gxf2bed provides 3 new optional arguments: parent, child, feature
• The parent argument can be used to specify the main node from which the new .bed file will be build. This could be interpreted as 'which feature (3rd column) I want my .bed file to be build from'
• The child argument can be used to specify the child node from the bed file. This can be interpreted as 'which lines will compose my parent node information'
• The feature argument can be used to specify what does gxf2bed will use as the names on the .bed file. Could be 'geneid', 'transcriptid' or anything you want. You just need to be sure that this feature is present in all parent and child lines.
• These new additions do not compromise the initial functionality.

- Rust
Published by alejandrogzi about 2 years ago

https://github.com/alejandrogzi/gxf2bed - v0.1.0

v0.1.0

- Rust
Published by alejandrogzi about 2 years ago