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Provide a way to specify a custom Deflater #109

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akiezun opened this issue Jul 1, 2016 · 0 comments
Open

Provide a way to specify a custom Deflater #109

akiezun opened this issue Jul 1, 2016 · 0 comments

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@akiezun
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akiezun commented Jul 1, 2016

htsjdk allows for specifying custom deflaters for writing bam files. We (GATK) would like to use the IntelDeflater from the Intel GKL https://github.com/Intel-HLS/GKL

This can be done by setting BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory()); or by setting the right deflater on the writers
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