This repository contains test data needed for running tests within the GOR repository. The following sections contain details on this data.
External
The "external" directory contains data from other open source projects:
-
/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.
-
/samtools
This data originates from the samtools project found at: https://github.com/samtools/htsjdk This project is under MIT License.
-
/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