I am still curious... why was this broken?
I know IGB supports synonyms for chromosome names and I think it is supposed to support "Chr1" and "chr1" for the A. thaliana genome. Might this test have been designed to test that the synonym system is working? And the test failing is indicating that the synonym system is NOT working...? I doesn't say that, but this file is pretty void of comments, so we have to make assumptions about what each test is designed to test for.
In an older version (8.2.3) the chromosome names that display in the A. thaliana genome are lower cased, "chr1".
This is odd, given that IGB doesn't store data. So both versions that I have running next to each other (v8.2 and v9.0) should be looking at the same data, because they are looking at the same remote quickload site. But in v8.2 shows "chr1" and v9.0 shows "Chr1".
The "Chr1" is a more accurate reflection of what is in the genome file. So how does v8.2 have "chr1" ?
The user's guide talks about making a chromosomes.txt file with synonyms for chromosome names.
https://wiki.transvar.org/display/igbman/Personal+Synonyms
I think IGB has a built-in chromosomes.txt file.
I think there must have been a change in that file or the code that uses it.
We should test the synonyms functionality.
The current solution is good. It checks that the expected chromosome names are present (based on the names they have in the sequence file). And making the test pass allows all of the subsequent tests to run.
Link to this branch on Bitbucket:
https://bitbucket.org/jdaly8/integrated-genome-browser/branch/IGBF-1142