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), raw/annotated VCF files (variants-annotated.vcf) and genotyping VCF files (genotype_*.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 3.19 and Java 11 or higher is required.
• Installing
• How to use
• ​Apache Lucene homepage

License

​GNU Affero General Public License version 3

Download

Version	Revision	Date	Binary (tar.gz)	BASE Version*
1.6	6766	June 3, 2022	varsearch-1.6.tar.gz​ (5.7MB)	3.19	changelog
1.5	6570	February 2, 2022	varsearch-1.5.tar.gz​ (5.1MB)	3.18	changelog
1.4	6534	December 21, 2021	varsearch-1.4.tar.gz​ (5.1MB)	3.18	changelog
1.3	6417	September 20, 2021	varsearch-1.3.tar.gz​ (5.0MB)	3.18	changelog
1.2	6401	September 16, 2021	varsearch-1.2.tar.gz​ (5.0MB)	3.18	changelog
1.1	6287	June 11, 2021	varsearch-1.1.tar.gz​ (5.0MB)	3.18	changelog
1.0	6266	May 28, 2021	varsearch-1.0.tar.gz​ (5.0MB)	3.18	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 1.6 version:

svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/tags/1.6 varsearch-1.6

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

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