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karel-brinda / rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
http://karel-brinda.github.io/rnftools
MIT License
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ArtIllumina's number_of_read_tuples does not work #68

Open simonepignotti opened 6 years ago

simonepignotti commented 6 years ago

The parameter number_of_read_tuples to specify the number of reads to generate in rnftools.mishmash.ArtIllumina does not work. In the zip file there is an example for E. Coli which should generate 10 reads, but the final output actually contains 12.

test_art.zip

simonepignotti commented 6 years ago

This could be easily corrected by using the new art parameter -c (number of reads) instead of converting it to coverage as it was needed with the previous versions. I have implemented it in the pull request #67 (commit 5795e1b), but unfortunately it simulates N reads per contig. In the zip file there is an example where it generates exactly 10 reads for test_art.fa, but by duplicating the single contig in test_art.fa and running the same command on test_art_double.fq, it generates 20.

test_art_double.zip