specify that numbers of rejected reads are numbers of rejected reads...

[yannickwurm]

Hi John,

hope all is well for you.

I'm testdriving your approach. Initially I was using mapping-based approaches, but it turns out that the "non-reference-genome" allele is often missed. Thus an approach such as yours (followed by subsequent mapping to reference genome) may be more defendable.

Quick useability comment: When running radpools -v, you may want to specify that numbers on the right are rejected reads. Its unclear from the standard output:
OK: 6743812 | FASTQ: 0 | RAD: 0 | Res: 422995 | MID: 33192 | Short: 0

cheers & all the best,
yannick

[johnomics]

Fixed in version 1.2.1; added total number of rejected reads to output