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nlapier2 / Metalign

Metalign: efficient alignment-based metagenomic profiling via containment min hash
MIT License
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FASTA and FASTQ support #3

Closed dkoslicki closed 5 years ago

dkoslicki commented 5 years ago

It appears KMC is expecting FASTQ formatted input in these lines:

KMC/bin/./kmc -v -k60 -fq -ci2 -cs3 -t48 -jlog_sample test/small_cami_low.fasta test/reads_60mers test/
Error: some error while reading fastq file, please contact authors

yet

KMC/bin/./kmc -v -k60 -fa -ci2 -cs3 -t48 -jlog_sample test/small_cami_low.fasta test/reads_60mers test/

runs just fine.

We should either specify in the man page that FASTQ is expected, or else add functionality to handle either FASTA or FASTQ (the better choice).

nlapier2 commented 5 years ago

Good suggestion. I've added the option for the user to specify either one, with the default being attempted auto-detection based on file name extension.