@benedictpaten Hoping this is a patch for your issue with the .tai index filtering out empty rows.
The tests still fail. This is because I'm using mafExtractor as a baseline to compare against. So it extracts a bunch of regions with mafExtractor (from mafTools) and then does the same queries with taffy view -r then diff's the results. They are now different because mafExtractor filters empty rows (which, while not illegal, are usually frowned on in MAF). I will change up the tests, but the current commit may be useful in the meantime...
@benedictpaten Hoping this is a patch for your issue with the .tai index filtering out empty rows.
The tests still fail. This is because I'm using
mafExtractoras a baseline to compare against. So it extracts a bunch of regions withmafExtractor(frommafTools) and then does the same queries withtaffy view -rthendiff's the results. They are now different becausemafExtractorfilters empty rows (which, while not illegal, are usually frowned on in MAF). I will change up the tests, but the current commit may be useful in the meantime...