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Remove GenomeLocParser from BaseTest #2125

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lbergelson opened this issue Aug 26, 2016 · 0 comments
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Remove GenomeLocParser from BaseTest #2125

lbergelson opened this issue Aug 26, 2016 · 0 comments
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@lbergelson
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BaseTest instantiates a GenomeLocParser that uses one of our test references. This causes BaseTest to be unusable by external projects that don't have the file included. We should either package the reference file in the jar or we should remove the GenomeLocParser from BaseTest and instantiate it in the classes that actually use it.
@lbergelson lbergelson mentioned this issue Aug 26, 2016
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@magicDGS magicDGS mentioned this issue Sep 8, 2016
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@droazen droazen added this to the 4.0 release milestone Mar 22, 2017
This was referenced Jun 27, 2017
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Closed
@magicDGS magicDGS mentioned this issue Aug 22, 2017
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@droazen droazen removed this from the Engine-4.0 milestone Oct 17, 2017
lbergelson pushed a commit that referenced this issue Nov 1, 2017
@magicDGS @lbergelson
create GATKBaseTest so downstream projects can use BaseTest #2125 #3029…
9283269 
… (#3475)

Projects depending on GATK have had trouble using BaseTest because it tries to load specific files from the gatk test resources.  If the project didn't include these files, the tests would crash.  This separates out a new GATK only GATKBaseTest which contains all of the file references but leaves the useful utilities in BaseTest for downstream use.

It makes similar changes in other test classes that had related issues.
fixes #2125 
fixes #3029
Introduces #3771 but due to the pain of rebasing the entire test suite repeatedly, this will be addressed in a follow up PR.  

* Factor out a GATKBaseTest for separate test resources from test utilities in BaseTest
* Repackage CommandLineProgramTest due to project-specific paths
* Refactor TargetsToolsTestUtils to allow downstream projects to use with custom references
jonn-smith pushed a commit that referenced this issue Nov 27, 2017
@magicDGS @jonn-smith
create GATKBaseTest so downstream projects can use BaseTest #2125 #3029…
a003f95 
… (#3475)

Projects depending on GATK have had trouble using BaseTest because it tries to load specific files from the gatk test resources.  If the project didn't include these files, the tests would crash.  This separates out a new GATK only GATKBaseTest which contains all of the file references but leaves the useful utilities in BaseTest for downstream use.

It makes similar changes in other test classes that had related issues.
fixes #2125
fixes #3029
Introduces #3771 but due to the pain of rebasing the entire test suite repeatedly, this will be addressed in a follow up PR.

* Factor out a GATKBaseTest for separate test resources from test utilities in BaseTest
* Repackage CommandLineProgramTest due to project-specific paths
* Refactor TargetsToolsTestUtils to allow downstream projects to use with custom references
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