support gzip'd input fasta

medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

http://medvedevgroup.com/

Other

141 stars 19 forks source link

support gzip'd input fasta #38

Open nick-youngblut opened 2 years ago

nick-youngblut commented 2 years ago

Running SibeliaZ v1.2.4 on gzip'ed input fasta files results in the following error:

Error: The FASTA header should start with a '>', started with ''
Loading the graph...
error: Can't read the input file

Given that the user will almost definitely have their genome fasta files gzip'ed if they have 100's or 1000's (or more), it would be great if SibeliaZ supported gzip'ed (and maybe bzip2) compressed input.

iminkin commented 2 years ago

Hi,

Thank you for the suggestion! I will include it in the next release.