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[ADAM-1697] Expand Illumina metadata regex to cover index sequences #2004

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merged 2 commits into from Jun 28, 2018

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pauldwolfe commented Jun 28, 2018

Now includes possible index sequence characters.

Paul Wolfe Paul Wolfe
[ADAM-1697] Expand illumina metadata regex
Now includes possible index sequence characters.
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AmplabJenkins commented Jun 28, 2018

Can one of the admins verify this patch?

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pauldwolfe commented Jun 28, 2018

This change was discussed in gitter with @heuermh (actually he made the change, I just wrote the test and added the test resources). Perhaps he can review it.

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+1, thanks for the addition!


sparkTest("Paired read names with index sequences in read names can grouped into fragments") {
val path1 = testFile("read_names_with_index_sequences_pair1.fq")
val path2 = testFile("read_names_with_index_sequences_pair1.fq")

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heuermh Jun 28, 2018

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I think this line should be "read_names_with_index_sequences_pair2.fq"

@heuermh heuermh changed the title [ADAM-1697] Expand illumina metadata regex [ADAM-1697] Expand Illumina metadata regex to cover index sequences Jun 28, 2018

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heuermh commented Jun 28, 2018

Fixes #1697

Paul Wolfe Paul Wolfe
[ADAM-1697] Expand illumina metadata regex
Fix typo in unit test.
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pauldwolfe commented Jun 28, 2018

Fixed change request from @heuermh

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heuermh commented Jun 28, 2018

Thank you, @pauldwolfe!

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heuermh commented Jun 28, 2018

Jenkins, test this please

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heuermh commented Jun 28, 2018

Jenkins, add to whitelist

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AmplabJenkins commented Jun 28, 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/2776/
Test PASSed.

@heuermh heuermh merged commit e7cbfcd into bigdatagenomics:master Jun 28, 2018

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Codacy/PR Quality Review Up to standards. A positive pull request.
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heuermh commented Jun 28, 2018

Squashed and merged as commit e7cbfcd, thank you, @pauldwolfe!

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