NIO output support for HaplotypeCaller #4721
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Codecov Report
@@ Coverage Diff @@
## master #4721 +/- ##
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Coverage 80.124% 80.124%
Complexity 17436 17436
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Files 1082 1082
Lines 63150 63150
Branches 10187 10187
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Hits 50598 50598
Misses 8568 8568
Partials 3984 3984
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@droazen this is ready for review! |
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ping? It's been a little while, a review would be nice. If @droazen is busy, perhaps @lbergelson can have a look? |
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@jean-philippe-martin I'll try to get to this one this week |
jamesemery
requested changes
May 14, 2018
| @@ -10,6 +10,7 @@ | |||
| import htsjdk.samtools.util.Locatable; | |||
| import htsjdk.samtools.SamFiles; | |||
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| import java.nio.file.Path; | |||
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You should add a test (either here or in HaplotypeCallerIntegrationTest which asserts that the tool can actually write into the test bucket (similar to the ApplyBQSRIntegrationTest.testApplyBQSRCloud() test you wrote for a one of your other branches).
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OK, I added it to HaplotypeCallerIntegrationTest, in the "bucket" group.
jamesemery
approved these changes
May 21, 2018
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Awesome, @jamesemery, thank you very much! |
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HaplotypeCaller's bamOutputPath is no longer internally converted to a File so "gs://" paths can now be passed for the optional "bam output" parameter.