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palindrome ITR artifact transformer skips reads whose contigs are not in sequence dictionary #6968

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merged 1 commit into from
Jan 26, 2022
Merged

palindrome ITR artifact transformer skips reads whose contigs are not in sequence dictionary #6968

merged 1 commit into from
Jan 26, 2022

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davidbenjamin
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Closes #6851. @fleharty

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gatk-bot commented Nov 18, 2020 •
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Travis reported job failures from build 32164
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk8 32164.1 logs
cloud openjdk8 32164.1 logs

fleharty
fleharty previously requested changes Jan 28, 2021
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Please create a test that fails on the previous code, and succeeds on the current code.

@lbergelson lbergelson changed the title palindorme ITR artifact transformer skips reads whose contigs are not in sequence dictionary palindrome ITR artifact transformer skips reads whose contigs are not in sequence dictionary Mar 17, 2021
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@davidbenjamin I think we are just waiting on a test for this. Is there any other reason this is blocked?

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@fleharty No other reason. Genevieve requested data from the user and has yet to hear back.

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@takutosato We are never going to hear from the user, but it's not a bad bug fix. Could you review this?

@davidbenjamin davidbenjamin assigned takutosato and unassigned fleharty Jan 24, 2022
takutosato
takutosato approved these changes Jan 26, 2022
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Looks good!

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Review notes:

IMG-0427
:

@davidbenjamin davidbenjamin dismissed fleharty’s stale review January 26, 2022 18:06

Never got data from user, couldn't reproduce error

@davidbenjamin davidbenjamin merged commit 4cbff5d into master Jan 26, 2022
@davidbenjamin davidbenjamin deleted the db_palindrome branch January 26, 2022 18:06
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@takutosato takutosato takutosato approved these changes

@fleharty fleharty fleharty left review comments

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Mutect2 BAM contigs not in reference
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@davidbenjamin @gatk-bot @fleharty @takutosato