Changing the name of the GencodeFuncotationFactory to be read from file. #4823
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LeeTL1220
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May 29, 2018
| @@ -203,24 +203,24 @@ private static void addManualAnnotationsToArguments(final ArgumentsBuilder argum | |||
| true, | |||
| FuncotatorTestConstants.REFERENCE_VERSION_HG19, | |||
| }, | |||
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Can you remove commented code or file an issue that it should be uncommented and when?
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It should not be commented out - I just wanted to disable some of the tests. Fixed.
| @@ -165,26 +175,27 @@ | |||
| // Constructors: | |||
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| public GencodeFuncotationFactory(final Path gencodeTranscriptFastaFile, final String version) { | |||
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If the constructors use DEFAULT_NAME doesn't this mean that the config file will be ignored? Or is the constructor with the name parameter the only one that is used? Can you delete some of the other constructors?
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The constructor that was being called in the code was the one that took a name. I deleted the other constructors for clarity as suggested.
Fixes #3956 Now gencode data sources have names preserved from config files. Updated MafOutputRenderer to put a space and delimiter between the date and first funcotation factory information. Updated some test cases to be correct with the new Gencode name preservation and MAF renderer update. Addressed code review comments.
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Codecov Report
@@ Coverage Diff @@
## master #4823 +/- ##
===============================================
- Coverage 80.332% 78.513% -1.819%
+ Complexity 17625 17444 -181
===============================================
Files 1088 1088
Lines 63849 64601 +752
Branches 10276 10475 +199
===============================================
- Hits 51291 50720 -571
- Misses 8558 9877 +1319
- Partials 4000 4004 +4
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Fixes #3956
Now gencode data sources have names preserved from config files.
Updated MafOutputRenderer to put a space and delimiter between the date and first funcotation factory information.
Updated some test cases to be correct with the new Gencode name preservation and MAF renderer update.