= Variant Search extension =

This package is an extension package to BASE that implements
a variant search engine for the variant calling results created
be the Reggie variant calling pipeline. The search engine can also
be used on the Relax server.

The search engine takes the filtered VCF files (`variants-filtered.vcf`) 
that are linked to the `VariantCall` raw bioassays and creates a searchable 
index for all variants. The indexing and search functionality is provided
by Apache Lucene.
 

== Documentation ==

 * BASE 3.18 and Java 11 or higher is required.
 * [wiki:net.sf.basedb.varsearch/install Installing]
 * [wiki:net.sf.basedb.varsearch/using How to use]
 * [https://lucene.apache.org/ Apache Lucene homepage]


== License ==

[http://www.gnu.org/licenses/agpl-3.0.html GNU Affero General Public License version 3]


== Download ==

|| '''Version''' || '''Revision''' || '''Date'''        || '''Binary (tar.gz)''' || '''BASE Version'''* ||  ||
|| 1.2           || 6401           || September 16, 2021 || [attachment:wiki:net.sf.basedb.varsearch:varsearch-1.2.tar.gz?format=raw varsearch-1.2.tar.gz] (5.0MB) || 3.18 || [query:"group=resolution&milestone=Variant Search v1.2&order=priority" changelog] ||
|| 1.1           || 6287           || June 11, 2021 || [attachment:wiki:net.sf.basedb.varsearch:varsearch-1.1.tar.gz?format=raw varsearch-1.1.tar.gz] (5.0MB) || 3.18 || [query:"group=resolution&milestone=Variant Search v1.1&order=priority" changelog] ||
|| 1.0           || 6266           || May 28, 2021 || [attachment:wiki:net.sf.basedb.varsearch:varsearch-1.0.tar.gz?format=raw varsearch-1.0.tar.gz] (5.0MB) || 3.18 || [query:"group=resolution&milestone=Variant Search v1.0&order=priority" changelog] ||


'''*''' In general, each release works with the specified and later BASE versions.

'''Source code''' can be downloaded from the subversion repository. Use the following command to get source code for the 1.1 version:

 `svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/tags/1.2 varsearch-1.2`


The latest development (''maybe unstable; do not use on a production server'') revision can be checked out from the repository using the following command:

 `svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/trunk varsearch-dev`



== Contribute ==

After making modifications to the source code, compose a clear and concise log message to describe those changes and the reasons for them. Then, send an email to the developers list containing your log message and the output of svn diff (from the top of your subversion working copy). If the community members consider your changes acceptable, someone who has commit privileges will add your changes to the public source code tree. Recall that permission to directly commit changes to the repository is granted on merit - if you demonstrate comprehension of subversion, programming competency, and a ''team spirit'', you will likely be awarded that permission.


== Todo ==
[[TicketQuery(status!=closed&component=net.sf.basedb.varsearch)]]