Leighton Pritchard

Thanks @peterjc - that's a considerable speed-up, and worth considering as a drop-in replacement for PrimerSearch - it could have a significant effect on runtime. A quick Google suggests it's...

> I recently emailed Jim Kent about a trivial bug (one of the documented options is not implemented), partly to see if he replies. Putting this in a positive light,...

> Large genome example, 173 contigs in 116MB FASTA file, with 2634 candidate primers (only 2300 unique), simple test script: > Best of 5 with ispcr: ``` real 0m2.678s user...

Hi @aiqubo - thank you for your interest in `pdp`. I don't see from your issue how you acquired `pdp`. Did you clone the repository? If so, what is the...

> Hi Leighton - thank you for feedback, > I'm more interested in the new version > I download pdp use 'git clone https://github.com/widdowquinn/find_differential_primers' > > qubo Apologies for the...

Yes - thankyou for the prompt - I'll do that shortly for the 'old' script. There will be a 0.2.0 release coming along soon, too - with the `diagnostic_primers` branch...

I'd say "delayed" rather than overdue, only because I didn't state a deadline date ;) Less flippantly, it's one of many ongoing things - the `diagnostic_primers` branch is usable, but...

That's [v0.1.4](https://github.com/widdowquinn/find_differential_primers/releases/tag/v0.1.4) released - `conda` package to follow shortly.

As an implementation, a first thought is: - all-vs-all genome comparisons with `mummer` - for each genome with `CLASS` - collect alignments against non-`CLASS` genomes as intervals on the query...

At the moment, the quickest way to get past this is to remove that sequence from the config file (as you've done). I'm in the middle of a major rewrite,...