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Merge new testing code into devel

Closed Merge new testing code into devel
testing into devel
1 unresolved thread
Closed van den Berg requested to merge testing into devel
1 unresolved thread

This fixes both #5 and #6.

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Pipeline #2865 failed

Stage: test

Pipeline failed for e6309163 on testing

Closed by van den Bergvan den Berg 5 years ago (Nov 26, 2019 7:13am UTC)

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vtools/cli.py
32 32 "May be called multiple times",
33 33 required=True)
34 34 @click.option("-s", "--stats", type=click.Path(writable=True),
35 help="Path to output stats json file", required=True)
35 help="Path to output stats json file", default='-')
  • Ruben Vorderman added 1 commit

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  • Ruben Vorderman added 1 commit

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  • Ruben Vorderman added 1 commit

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  • van den Berg added 2 commits

    added 2 commits

    • 51eb6db9 - Do not use '-' as a stand in for stdout
    • 2fda84f6 - Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing

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  • van den Berg added 1 commit

    added 1 commit

    • fb075df9 - Compare allele genotypes directly

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  • van den Berg added 5 commits

    added 5 commits

    • 9e87861b - Add check for phased calls
    • 3479a77a - Convert single use fixtures to regular tests
    • 86bd745b - Add check for decomposed calls
    • 05ade21d - Clean up test data
    • 8786b514 - Add check for non-diploid calls

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  • van den Berg added 2 commits

    added 2 commits

    • d6a8d0e5 - Extract genotypes to support conflicting ALT calls
    • f9aadab3 - Add support for parital calls

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  • van den Berg added 1 commit

    added 1 commit

    • b63f7cb0 - Add test cases where the ALT and REF differ

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  • van den Berg added 2 commits

    added 2 commits

    • bbb226bc - Add test for a rare bug with partial variants
    • 0ab4c701 - Fixed bug with partial no calls

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  • van den Berg added 1 commit

    added 1 commit

    • 955802ec - Add test cases for missing ALT in call vcf

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  • van den Berg added 2 commits

    added 2 commits

    • d37115cc - Add support for RQC annotations to be used as GQ
    • c76505da - Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing

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  • van den Berg added 1 commit

    added 1 commit

    • b151b5db - Write discordant variants to valid vcf file

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  • van den Berg added 5 commits

    added 5 commits

    • d6779d59 - tox automatically calls pip install '.'
    • 3c789431 - Update min-depth to integer
    • 257600ce - Write to stats file instead of using print
    • e62c9164 - Use get_header_type to determine if RGQ is present
    • e6309163 - The discordant VCF file is gzipped

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  • van den Berg closed

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