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gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
MIT License
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Large genome or large chromosome #125

Open xiekunwhy opened 11 months ago

xiekunwhy commented 11 months ago

Hi,

I found that gffread (v0.12.7.) can not deal with large chromosomes, we may find minus coordinates when using gffread to deal with such large chromosomes, for example, for a genome here https://ftp.cngb.org/pub/CNSA/data5/CNP0003098/CNS0560369/CNA0050666/ when I ran gffread -T -o file2.gtf MD.chromosome_level.gene.gff I got many minus coordinates, what's wrong? image

Best, Kun

gpertea commented 11 months ago

This is an issue related to the internal representation of coordinates as a 32bit integer. I will have to update my code to use 64 bit instead, in order to support giga-chromosomes larger than 2 billion bases (2Gb).

xiekunwhy commented 11 months ago

Hope new version comming soon, we are now dealing with several long-chromosome genomes.

xiekunwhy commented 6 months ago

Hope the update version comming soon, as more and more species with giga-chromosomes were published.