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Load vcf bgz #238

Merged
merged 7 commits into from
Apr 15, 2024
Merged

Load vcf bgz #238

merged 7 commits into from
Apr 15, 2024

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ChristinaXu2017
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@ChristinaXu2017 ChristinaXu2017 commented Apr 4, 2024 •
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  • created a java method au.csiro.variantspark.utils. FileUtils.isBGZFile(String filePath).

    • it checks whether an input file is VCF BGZP file or not.
    • it calls method of BlockCompressedInputStream.isValidFile(bufferedInputStream);

  • apply above method to au.csiro.variantspark.cli.args.SparkApp.textFile(inputFile: String)

    • it calls sc.textFile(...) for non BGZIP input
    • it calls sc.parallelize(...) for BGZIP input

  • regression test may require to be update to test input in .vcf, .vcf.bz2, .vcf.gz and .vcf.bgz

bhosking
bhosking reviewed Apr 5, 2024
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Just some cleaning up, the logic is fine.

src/main/java/au/csiro/variantspark/utils/FileUtils.java Outdated Show resolved Hide resolved
src/main/java/au/csiro/variantspark/utils/FileUtils.java Outdated Show resolved Hide resolved
src/main/java/au/csiro/variantspark/utils/FileUtils.java Outdated Show resolved Hide resolved
src/main/scala/au/csiro/variantspark/cli/args/SparkArgs.scala Show resolved Hide resolved
ChristinaXu2017
ChristinaXu2017 commented Apr 11, 2024
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@ChristinaXu2017 ChristinaXu2017 left a comment

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Hi Brendon, could you please approve this pull request if no further action requires.

@bhosking bhosking merged commit 2fb2642 into master Apr 15, 2024
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@bhosking bhosking deleted the load_vcf_bgz branch April 15, 2024 04:17
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