Is --repair available?

[jasonsydes]

Hi there primalscheme developers,

We were curious if the "--repair" feature described here will be published to this github repository? We'd like to utilize it.

Thank you!

[aresti]

Hi Jason,

I've actually built this option into a new codebase (a complete rewrite of primalscheme). Its currently in a separate repo that we haven't made public. The intention is to make this public as soon as possible, pending experimental validation and completion of the automated test suite.

That being said, we'd be happy to run it for you in the mean time if you could email us over your old primer bed file and a new input ref fasta?

Cheers,
Andy

[jasonsydes]

Hi Andy, Aha! Interesting! Yes, we would very much like to send you our BED file and a multi-fasta with omicron and some other variants. What email address should I send it to? Feel free to reply here on github, or to send it to my email address, which is sydes at uoregon dot edu. Thank you!! Jason

…

On Tue, Dec 7, 2021 at 5:47 AM Andy Smith ***@***.***> wrote: Hi Jason, I've actually built this option into a new codebase (a complete rewrite of primalscheme). Its currently in a separate repo that we haven't made public. The intention is to make this public as soon as possible, pending experimental validation and completion of the automated test suite. That being said, we'd be happy to run it for you in the mean time if you could email us over your old primer bed file and a new input ref fasta? Cheers, Andy — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/aresti/primalscheme/issues/30*issuecomment-987940766__;Iw!!C5qS4YX3!RNFF7cp6DqSzNLacu0d6za652-BsfY1JZ92SDgvEWsmd6FJ2CkDkQUK9pnfidhTF$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AABMTLWHRVH54T75XLJMS53UPYF4VANCNFSM5JPZVURA__;!!C5qS4YX3!RNFF7cp6DqSzNLacu0d6za652-BsfY1JZ92SDgvEWsmd6FJ2CkDkQUK9plE6s8SZ$> . Triage notifications on the go with GitHub Mobile for iOS <https://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!C5qS4YX3!RNFF7cp6DqSzNLacu0d6za652-BsfY1JZ92SDgvEWsmd6FJ2CkDkQUK9pvB2fQR4$> or Android <https://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!C5qS4YX3!RNFF7cp6DqSzNLacu0d6za652-BsfY1JZ92SDgvEWsmd6FJ2CkDkQUK9piiHIJLG$>.

[Coppini]

Is there any updates on the new codebase/release/rewrite?
Either for the --repair mode or the reference masking mentioned by @joshquick on the Artic workshop?
Thanks!

[aresti]

Sorry for the delay in getting back to you. We’re aiming to open this up for people who wish to test hopefully next week. We’ll add you to the repos for primalscheme2 and the reference masking pipeline in due course. Cheers, Andy

[Coppini]

Any further updates on primalscheme2? I'd be happy to contribute on testing it or even with the code if there's anything I can help with. We're looking forward to using that --repair mode you mentioned in the workshop. 😄