Jerome Kelleher
Jerome Kelleher
In the data downloader script, some fields (e.g. `Reference.sourceUri` and Reference.sourceDivergence``) are set to null which is incompatible with protobuf.
Currently the OntologyTermMap silently returns the empty string when a term name cannot be found in the map. This is very problematic behaviour for an administrator, as they will not...
Assumes #1166 has been merged. Currently `getNameFromPath(filePath)` returns `filepath.split(".")[0]`, which is simple, but probably not what people expect for a lot of things. How should it work? Or should object...
Metadata input from the data repository is not type checked, which can lead to mysterious server failures at run time (this happens when we run the proto based server against...
We need some simple way of simulating G2P data so that we can include tests for it in the standard layout. This should include the standard tests in `tests/test_simulated_stack.py`.
The `testInstantiation` in `tests.unit.test_faultydata.TestDuplicateCallSetId` is currently disabled because it provokes an error that results in htslib aborting. This is a bug in htslib. We should: (a) track down where in...
Assumes #1166 has been merged. See TODO comments on lines 597 and 605.
Assumes #1166 has been merged. Currently the VariantAnnotations code is quite strict about the versions of the programs that it will support. We have ``` ANNOTATIONS_VEP_V82 = "VEP_v82" ANNOTATIONS_VEP_V77 =...
We will need to do this at some point, so opening issue to track.
It appears that Sqlite is flushing to disk quite aggressively, which makes importing large pedigree databases extremely slow. Even on an SSD, it takes a very long time to run...