fix: not erroring out when a non-ACGT base is in the query file #22
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which is very common
… to make Mac OS builds work
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Right now if there is even a single non-ACGT base in the query file,
COBSwill fail with:This is quite annoying as it is extremely common to have
Ns or other non-ACGT bases in assembly, contig, reads files, etc... I'd sayCOBSquery would actually fail more than succeed on random real-data query files.This PR is a first approach to solve this issue. It simply replaces non-ACGT bases by A. This is what is done MOF-search (https://github.com/karel-brinda/mof-search) and it is an ok approach. Maybe a better approach would be to randomise this replacement character, or receive it as a parameter, or actually skip the kmers, etc, etc... there are many approaches to deal with this that can be discussed and implemented later, but I think it is important to have a first solution to this.