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added test class for CheckFingerprint #1006

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merged 1 commit into from Dec 15, 2017
Merged

added test class for CheckFingerprint #1006

merged 1 commit into from Dec 15, 2017

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a-filipp0v
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Description

Added:

  • CheckFingerprintTest class;
  • fingerprinting_detail_metrics.example & fingerprinting_summary_metrics.example files in /testdata/picard/fingerprints as correct examples.

Checklist (never delete this)

Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.

Content

  • Added or modified tests to cover changes and any new functionality
  • Edited the README / documentation (if applicable)
  • All tests passing on Travis

Review

  • Final thumbs-up from reviewer
  • Rebase, squash and reword as applicable

For more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests

yfarjoun
yfarjoun suggested changes Dec 15, 2017
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looks good! thanks for testing.

some minor comments.

src/test/java/picard/fingerprint/CheckFingerprintTest.java Outdated
"H=" + SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING
};
Assert.assertEquals(runPicardCommandLine(args), 0);
Assert.assertEquals(checkResult(
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I think it would be better to have two asserts, one for each metrics file....that way when something breaks it's easier to understand where the probem is

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Done!

src/test/java/picard/fingerprint/CheckFingerprintTest.java Outdated
new File(TEST_DATA_DIR + "/tempCheckFPDir/detail")), true);
}

@Test(dataProvider = "badData", expectedExceptions = {TribbleException.MalformedFeatureFile.class,
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is the fully qualified class name needed?

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coveralls commented Dec 15, 2017 •
edited

Coverage Status

Coverage increased (+0.4%) to 77.634% when pulling c412469 on EpamLifeSciencesTeam:epam-ls_tests_for_CheckFingerprint into b0b9f78 on broadinstitute:master.

@a-filipp0v
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Hello, thanks for your feedback!
Made few changes in accordance with your comments:

  • removed checkResult method, it’s invocation has been replaced by two asserts, one for each metrics file;
  • full names of exceptions were replaced by short ones, corresponding imports added;
  • few cosmetic changes, removed unnecessary throws from methods’ signature.

@a-filipp0v a-filipp0v force-pushed the epam-ls_tests_for_CheckFingerprint branch from c412469 to 63a6ed1 Compare December 15, 2017 12:31
@a-filipp0v
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I'm sorry, had some troubles with git branch, so all my small local commits were shown. Have made force push with amend, which replaced all of them with the last one.

All mentioned changes are inside.

Sorry for inconvenience.

Changes:
e781bd7 
- removed checkResult method, it’s invocation has been replaced by two asserts, one for each metrics file;
- full names of exceptions were replaced by short ones, corresponding imports added;
- few cosmetic changes, removed unnecessary throws from methods’ signature.
@a-filipp0v a-filipp0v force-pushed the epam-ls_tests_for_CheckFingerprint branch from 63a6ed1 to e781bd7 Compare December 15, 2017 12:49
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coveralls commented Dec 15, 2017 •
edited

Coverage Status

Coverage increased (+0.4%) to 77.634% when pulling e781bd7 on EpamLifeSciencesTeam:epam-ls_tests_for_CheckFingerprint into 70da387 on broadinstitute:master.

yfarjoun
yfarjoun approved these changes Dec 15, 2017
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Thanks!

@yfarjoun yfarjoun merged commit 4e62e69 into broadinstitute:master Dec 15, 2017
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@yfarjoun yfarjoun yfarjoun approved these changes

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