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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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jellyfish count returns empty file when using --min-qual-char on fasta file #35

Closed dkoslicki closed 9 years ago

dkoslicki commented 9 years ago

It appears that jellyfish (version 2.1.1) fails when using the flag --min-qual-char on a fasta file. For example, jellyfish count test.fasta -m 20 -s 100M -t 20 -Q C -o test.jf results in file test.jf with no kmers in it.

Perhaps it would be better for jellyfish to either throw an error when combining -Q with a fasta file, or else simply ignore the -Q flag (I think the latter might be better).

gmarcais commented 9 years ago

This is fixed. -Q has no effect on fasta files now. See latest release v2.2.3.

Thanks for the bug report.