Jerome Kelleher
Jerome Kelleher
When we are calculating the md5checksums for for each reference, we should have an INFO level output to keep the user informed, i.e., ``` $ ga4gh_repo -v add-referenceset test.db 1kg-data/human_g1k_v37.fasta.gz...
The file handle cache in `ga4gh/datamodel/__init__.py` provides a way for us to keep a cache of most recently used files, and opens new files on demand. This allows us to...
Assumes #1166 has been merged. We should check that the reference set that we have associated with ReadGroupSets and VariantSets are minimally consistent with the data they contain at import...
Assumes #1166 has been merged. The goal of the repo manager `verify` function is to let an administrator run some simple diagnostics on the repository. This is useful to check,...
We currently do not support returning unmapped reads, as this is hard to do with pysam. However, there is no test coverage to ensure that we are reporting this correctly....
There are multiple TODO items in the `ga4gh/datamodel/reads.py` file, particularly where we translate from pysam objects into the GA4GH equivalents (see the `convertReadAlignment` method). None of the current developers have...
The `tests/unit/test_faulty_data.py` module is used to test what happens when we provide bad input data to the server. The bad input data is stored in `tests/faultydata`. Add some malformed BAMS...
[CORS](https://en.wikipedia.org/wiki/Cross-origin_resource_sharing) support is required for servers to support JavaScript clients. Tests verifying the server's CORS support are in `tests/unit/test_views.py`, which tests other high-level HTTP related things (this test module is...
Simulated data is very important for testing, as discussed in #715. The simulator for reads is currently very crude. Some improvements we can make - Add some simulated programs. See...
Data driven tests allow us to test our translation code in the face of input data (see #713 for a description). We currently use pysam in our production code and...