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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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@fnothaft
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@fnothaft 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 coveralls commented Mar 7, 2018

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 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 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 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 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.

@@ -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

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

fnothaft Mar 7, 2018
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+1, SGTM

@fnothaft fnothaft force-pushed the fnothaft:issues/1939-info-flag branch from 7a7eae6 to 93b2510 Mar 7, 2018
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@AmplabJenkins 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.

@heuermh
heuermh approved these changes Mar 7, 2018
@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 heuermh commented Mar 7, 2018

Thank you, @fnothaft

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4 participants