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[ADAM-1476] Treat `.` ALT allele as symbolic non-ref. #1477

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merged 1 commit into from Apr 7, 2017

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@fnothaft
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@fnothaft fnothaft commented Apr 6, 2017

Resolves #1476.

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@coveralls coveralls commented Apr 6, 2017

Coverage Status

Coverage increased (+0.1%) to 81.637% when pulling b20dce2 on fnothaft:issues/1476-drop-.-alts into 9505d47 on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Apr 6, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1935/
Test PASSed.

@@ -182,31 +182,37 @@ class ADAMContextSuite extends ADAMFunSuite {
sparkTest("can read a gzipped .vcf file") {
val path = testFile("test.vcf.gz")
val vcs = sc.loadVcf(path)
assert(vcs.rdd.count === 6)
assert(vcs.rdd.count === 7)

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@heuermh

heuermh Apr 6, 2017
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were the compressed test resources changed too?

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@fnothaft

fnothaft Apr 6, 2017
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Nope... they appear to have been a compressed version of the VCF file from Hadoop-BAM.

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@heuermh
heuermh approved these changes Apr 6, 2017
@heuermh heuermh merged commit 93b32c6 into bigdatagenomics:master Apr 7, 2017
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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.1%) to 81.637%
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@heuermh
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@heuermh heuermh commented Apr 7, 2017

Thank you, @fnothaft!

@a1xt06
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@a1xt06 a1xt06 commented Apr 7, 2017

Thank you!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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