Sampling single reads failed

[suzuki-shm]

Hi,

When I used seqtk sample command with 1 as number of sequence, I didn't get a file that have single reads, but I got all of reads(=input sequence file).
This reproduced by multiple test sequence files and seeds.
The commands I used is

seqtk sample test_reads.fq 1

I ran it with CWL wrapped seqtk, and raw software inside docker container.

[shenwei356]

Try

 seqtk sample test_reads.fq 1.1

It works

[tseemann]

@TaskeHAMANO The number can be a fraction OR an exact number.
You have discovered an ambuguity with the string 1.
It could be 1 read, or ALL the reads (fraction 1.0).
@shenwei356 has a nice workaround - because fraction must be between 0 and 1, if you give it 1.1 it must be treating it as a number, and rounding it down to 1.

[eboyden]

I would actually prefer that 1.0 be treated as a float (returning all reads) rather than an int, whereas 1 would return a single read. I'd recommend enforcing this behavior, so that integers are treated as numbers and floats are treated as fractions. This could also be used to allow oversampling, e.g. 10 would return 10 reads but 10.0 would oversample 10X.