Fix using the "Color by modifications" setting on files that need ref renaming #2128
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Note that the way it is done here is also the way it is done e.g. on the wiggle get stats rpc call |
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@@ Coverage Diff @@
## main #2128 +/- ##
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Coverage 61.99% 61.99%
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Files 476 476
Lines 22781 22781
Branches 5351 5351
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Hits 14123 14123
Misses 8377 8377
Partials 281 281
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Fixes #2125
There is a subtle chain of behaviors where because the ref renaming didn't work, it created the invalid state seen in #2125
It started with the assemblyName not being defined, so renameRegionsIfNeeded returned the regions back, so then the bamadapter just returned 0 features for requests to the wrong chromosome for getting the 'modification color map' preprocessing step, so then the colors were black
complicated chain of events...it could be interesting if it used the assemblyName on the region object perhaps but this fixes the issue in the current way that things work