GOR Test Data

This repository contains test data needed for running tests within the GOR repository. The following sections contain details on this data.

bvl_min

Brown Violetta Demo case - reduced to a single gene (SLC25A2) with the causative variant.

External

The "external" directory contains data from other open source projects:

1. /bgen

   This data originates from from the bgen project found at: https://bitbucket.org/gavinband/bgen/src/default/example/ This project is under Boost Software License v1.0.

2. /samtools

   This data originates from the samtools project found at: https://github.com/samtools/htsjdk This project is under MIT License.

3. /gvcf

   Example gvcf file retrieved from https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

gor

Several example gor files used for testing:

• dbsnp files

    Several variations of the dbsnp data on gor format.
  

• ensgenes_exons.gorz -

    Example gor file with gene exon data.
  

• example.wgs.goodcov.gorz

    Example gor file with coverage data
  

• genes.gor & genes.gorz

   Example genes files on gor format containing gene information by chromosome and position.
  

• multicolumns.gor

   Example gor file with multiple columns
  

• singleposition.gorz

   Example gor file within only a single chromosome and position.
  

• too_many_seeks.gor

   Example gor file used for testing position caching.
  

nor

Simple nor files for testing nor file handling.

parquet

Example parquet files contain GOR data for testing parquet file handling by GOR. Documentation on parquet files can be found at: https://spark.apache.org/docs/latest/sql-data-sources-parquet.html

ref_mini

Mini reference data for testing (unit and integration). The reference data is minimized by approximately a factor of 1000

reports

Example yml files for running test reports