Remove workaround for gzip/BGZF compressed VCF headers #1057

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heuermh opened this Issue Jun 27, 2016 · 1 comment

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heuermh commented Jun 27, 2016

Remove the workaround here

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L159

for gzip/BGZF compressed VCF headers. The issue has been fixed upstream

Fix VCFHeaderReader for gzipped and BGZF VCF formats
HadoopGenomics/Hadoop-BAM#97

Note this will require bumping the dependency version of Hadoop-BAM to 7.5.1 (or 7.6.0) which may bring along a transitive dependency version bump of htsjdk to 2.5.0, see HadoopGenomics/Hadoop-BAM#107.

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heuermh Jul 26, 2016

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Fixed by #1060

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heuermh commented Jul 26, 2016

Fixed by #1060

@heuermh heuermh closed this Jul 26, 2016

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