Version 3.6.2 (Open Source release 1.2) of the APSampler

[favorov]

New version. Major.

The format of the statistics file changed. Thanks to Ramil Nurtdinov for the advice.

Now, the file is yaml and it is critically shorter than it was, for the same information.

The length of the key for statistics validation is also reduced, and eventually, it happens much faster.  

I hope, now it will work with 10000 variants.

Also, the table output format is added to the validation script.

Cheers,

Sasha.

http://apsampler.sourceforge.net/

[Vitaly Korchagin]

Hi!

I can't find the markup.pl script.

четверг, 31 января 2019 г. в 13:35:59 UTC+3, favorov:

[Alexander Favorov]

Please, can you remind me what is the script for? Did it disappear after 3.6.1 ?

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[Vitaly Korchagin]

https://sourceforge.net/p/apsampler/wiki/ReadmeTools/

MARKUP (using ONIONTREE) 

 This script is intended to markup the results of validation...

четверг, 27 августа 2020 г. в 04:04:28 UTC+3, favorov:

[Alexander Favorov]

Thank you. I'll check the things. Probably, we replaced it with
something and we did not update the documentation, Are you going to
use ONION XML?

On Thu, Aug 27, 2020 at 3:06 AM Vitaly Korchagin

> To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/48615355-0a9d-4837-b228-15239b8bc839n%40googlegroups.com.

[Vitaly Korchagin]

I would like to test a different output format for validation results. It may be XML, a table, or any structured format suitable for automatic parsing.

чт, 27 авг. 2020 г. в 10:40, Alexander Favorov <fav...@sensi.org>:

To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/CAEGYiUXS%2BT%2B67JY2dREy5GtiyErA1%2Bzht%3DyZyq%3DtNn8U9bYOOw%40mail.gmail.com.

[Alexander Favorov]

Got it.

On Thu, Aug 27, 2020 at 3:52 AM Vitaly Korchagin

> To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/CADZQoK5G-6CRQgi8H6eMD4Oxfh%3D1OUw3LJhrc3Lkx%2Bm47y-0zg%40mail.gmail.com.

[yankovsky]

Саша,

Спасибо за доверие быть включенным в группу интенсивно общающихся людей!

Не знаю кто и почему меня туда включил. Может быть включить меня туда когда пойму?

Коля Янковский

Отправлено со смартфона Samsung Galaxy.

-------- Исходное сообщение --------

От: Alexander Favorov <fav...@sensi.org>

Дата: 27.08.20 11:20 (GMT+03:00)

Кому: apsa...@googlegroups.com

Тема: Re: Version 3.6.2 (Open Source release 1.2) of the APSampler

To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/CAEGYiUWgLogYhO5Kd1-TQ6HrVhPN2p-%3D_csq1WDPJyzpZ3-DZw%40mail.gmail.com.

[Alexander Favorov]

Эта почтовая рассылка для пользователей прогрммы APSample .
http://apsampler.sourceforge.net/
Рабочие языки русский или английский. В этой рассылку я публикую
анонсы новых версий, их за последние 10 лет было две. Но в этом году
природа настолько очистилась, что здесь появились сообщения. Тут есть
соавторы проекта, коллеги, с которыми мы сотрудничаем, люди, которые
сами подписалались на рассылку через интерфейс Гугл, и люди, которых
явключал в эту рассылку, когда они по каким-то причинам интересовались
этим проектом. Мне кажется, я всех предупреждал все подписчиков, что
они подписчики, но, увы, точно уже не помню - рассылке много лет.
Извините за беспокойство, если что. Спасибо!

С приветом,
Саша.

This mailing list is about the APSampler software.
http://apsampler.sourceforge.net/
The languages are English and Russian. Usually, I publish announces
of the new versions here. There were two during the last decade.
Still, this year the environment went so clean, that messages appeared
there. The members of the group are the project coauthors, our
collaborators, people who subscribed through the google groups
interface, and people whom I have subscribed because they were
interested in the project. It seems to me I notified all the
subscribers that they are subscribers, but the list is really old and
I am not sure. I apologize for the inconvenience if any. Thank you!

Cheers,
Sasha

> To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/5f478727.1c69fb81.20dbc.183a%40mx.google.com.

[Alexander Favorov]

Hi Vitaly,
pleas, try -tsv or -tsv-car command-line switches for patterns_validation.pl
Sorry, it is a new feature and I did not reflect it in wiki yet.

Cheers,
Sasha.

On Thu, Aug 27, 2020 at 3:52 AM Vitaly Korchagin

> To view this discussion on the web visit https://groups.google.com/d/msgid/apsampler/CADZQoK5G-6CRQgi8H6eMD4Oxfh%3D1OUw3LJhrc3Lkx%2Bm47y-0zg%40mail.gmail.com.

[Vitaly Korchagin]

Ok. I tried it.

And a little question - How to explain patterns SNP*T and SNP*T,A or SNP*T,T? What "*" is mean? I assume SNP*T include all genotypes with T-alelle (homo- and heterozygote). Is it wrong?

суббота, 29 августа 2020 г. в 08:37:16 UTC+3, favorov: