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[ADAM-1939] Allow validation stringency to waive off FLAG arrays. #1940

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merged 1 commit into from Mar 7, 2018

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  0.24.0
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fnothaft commented Mar 7, 2018

Resolves #1939.

@fnothaft fnothaft added this to the 0.24.0 milestone Mar 7, 2018

@fnothaft fnothaft requested a review from heuermh Mar 7, 2018

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coveralls commented Mar 7, 2018 •
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Coverage Status

Coverage increased (+0.07%) to 82.532% when pulling 93b2510 on fnothaft:issues/1939-info-flag into f616784 on bigdatagenomics:master.
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coveralls commented Mar 7, 2018

Coverage Status

Coverage increased (+0.07%) to 82.545% when pulling 7a7eae6 on fnothaft:issues/1939-info-flag into 4e773c5 on bigdatagenomics:master.
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coveralls commented Mar 7, 2018

Coverage Status

Coverage increased (+0.07%) to 82.545% when pulling 7a7eae6 on fnothaft:issues/1939-info-flag into 4e773c5 on bigdatagenomics:master.
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coveralls commented Mar 7, 2018

Coverage Status

Coverage increased (+0.07%) to 82.545% when pulling 7a7eae6 on fnothaft:issues/1939-info-flag into 4e773c5 on bigdatagenomics:master.
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AmplabJenkins commented Mar 7, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2698/
Test PASSed.
adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala Outdated
@@ -482,14 +489,14 @@ class ADAMContextSuite extends ADAMFunSuite {
sparkTest("load vcf with a glob") {
val path = testFile("bqsr1.vcf").replace("bqsr1", "*")
val vcs = sc.loadVcf(path)
val vcs = sc.loadVcf(path, stringency = ValidationStringency.LENIENT)

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heuermh Mar 7, 2018

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Sorry to be a pain, could test files that are invalid be moved to a subdirectory so that the glob doesn't pick them up?

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fnothaft Mar 7, 2018

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+1, SGTM
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AmplabJenkins commented Mar 7, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2700/
Test PASSed.
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heuermh approved these changes Mar 7, 2018
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@heuermh heuermh merged commit bc8c6f4 into bigdatagenomics:master Mar 7, 2018
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Codacy/PR Quality Review Good work! A positive pull request.
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heuermh commented Mar 7, 2018

Thank you, @fnothaft
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