bed2gtf
A high-performance bed-to-gtf converter written in Rust.
// translates
chr27 17266469 17281218 ENST00000541931.8 1000 + 17266469 17281218 0,0,200 2 103,74, 0,14675,
// into
chr27 bed2gtf gene 17266470 17285418 . + . gene_id "ENSG00000151743";
chr27 bed2gtf transcript 17266470 17281218 . + . gene_id "ENSG00000151743"; transcript_id "ENST00000541931.8";
chr27 bed2gtf exon 17266470 17266572 . + . gene_id "ENSG00000151743"; transcript_id "ENST00000541931.8"; exon_number "1"; exon_id "ENST00000541931.8.1";
...
Converts
- *Homo sapiens* GRCh38 GENCODE 44 (252,835 transcripts) in 3.25 seconds.
- *Mus musculus* GRCm39 GENCODE 44 (149,547 transcritps) in 1.99 seconds.
- *Canis lupus familiaris* ROS_Cfam_1.0 Ensembl 110 (55,335 transcripts) in 1.20 seconds.
- *Gallus galus* bGalGal1 Ensembl 110 (72,689 transcripts) in 1.36 seconds.
> What's new on v.1.9.3
>
> - Fixes a bug with .gz decoder
> - Implements reading .bed.gz files!
> - Fixes bug described in issue #11 with versioning
## Usage
``` rust
Usage: bed2gtf[EXE] --bed/-b --isoforms/-i --output/-o