org.bdgenomics.adam.util

ADAMVCFOutputFormat

object ADAMVCFOutputFormat

A static object for attaching a header to the accompanying ADAMVCFOutputFormat hadoop writer. Categorically, this static attachment method is not good, and makes me feel unclean. Alack, there appears to be no workaround. Hadoop-BAM will not write a VCF to disk unless a header is attached, and Hadoop-BAM itself does not have a static way of attaching a header that works with the Spark Hadoop API writer.

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  6. def addHeader(vcfHeader: VCFHeader): Unit

    Attaches a header to the ADAMVCFOutputFormat Hadoop writer.

    Attaches a header to the ADAMVCFOutputFormat Hadoop writer. If a header has previously been attached, the header must be cleared first.

    vcfHeader

    Header to attach.

    Exceptions thrown
    Exception

    Exception thrown if a VCF header has previously been attached, and not cleared.

    See also

    clearHeader

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  8. def clearHeader(): Unit

    Clears the attached header.

    Clears the attached header.

    See also

    addHeader

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