accept lowercase bases

[JWDebler]

Hi there,
I just had rust-mdbg crashing on me with this error:

Non-ACGTN nucleotide encountered!Non-ACGTN nucleotide encountered!

Since CANU had no problems with my intput files I was surprised.
Took me a while to figure out that the problem was that the bases in my fastq files were in lowercase.

Any chance you could allow lowercase bases as input?
Cheers

[rchikhi]

hi, yes we'll fix the parser eventually, for now you can prepare your input using: seqtk seq -AU [yourfile.fasta/yourfile.fastq.gz]

[luizirber]

I added an issue to nthash to discuss how to solve this without needing to preprocess the input (and maybe avoid having to uppercase the sequence?)

[rchikhi]

good idea, thanks!