lskatz / fasten

:construction_worker: Fasten toolkit, for streaming operations on fastq files
MIT License
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fastq_mutate should always give -m mutations? #29

Closed telatin closed 9 months ago

telatin commented 10 months ago

for fasten_mutate is not clear if the number of SNPs should be guaranteed or it's just a maximum.

From the tests it looks like the second:

for i in {1..30}; 
do
  ./target/debug/fasten_mutate < testdata/four_reads.fastq  --snps 5 -m | awk 'NR % 4 == 2' | \
   sed 's/[a-z]//g' | perl -ne 'chomp; if (length($_)!=5){die "Error: unexpected SNPs count: $_\n"}'; 
done

If this is the intended behaviour I would specify so in the help page

 -s, --snps INT      Number of SNPs (point mutations) to include per read.

linked to #20