loadvcf: conflicting require statement #1094

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akmorrow13 opened this Issue Jul 31, 2016 · 1 comment

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akmorrow13 commented Jul 31, 2016

The requirement statement in loadVCF in ADAMContext line 634 is very misleading:

    // we can only replace the sequences header if the sequence info was missing on the vcf
    require(sdOpt.isEmpty || vcfSd.isEmpty,
      "Only one of the provided or VCF sequence dictionary can be specified.")

It says only one sequence dictionary is allowed to be specified but then it fails if only 1 sequence dictionary is empty. Is the or supposed to be an and?

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fnothaft Jul 31, 2016

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The require statement is correct; it will only fire if both SequenceDictionaries are populated and the expression evaluates to false. Can you send me a dataset/command line offline that reproduces the bug?

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fnothaft commented Jul 31, 2016

The require statement is correct; it will only fire if both SequenceDictionaries are populated and the expression evaluates to false. Can you send me a dataset/command line offline that reproduces the bug?

@akmorrow13 akmorrow13 closed this Jul 31, 2016

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