Fixes issue in BGZFSplitGuesser relating to incomplete copy. #149
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tomwhite
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Aug 25, 2017
fnothaft
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…plitGuesser Stems out of work done in HadoopGenomics#142 and HadoopGenomics#149. Refactors BGZFSplitGuesser to use the logic in the BaseSplitGuesser class. To do this, we need to make BaseSplitGuesser public. Additionally, we replace the logic that is used in BaseSplitGuesser to identify the start of a BGZF block with logic that doesn't require copying bytes from the input stream to a buffer. This improves the performance of identifying the start of a BGZF block; for whatever reason, that copy to the buffer/methods on the buffer are expensive.
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Supersedes #142. Uses fixed copying logic from
BAMSplitGuesser. I've done a quick set of tests using BGZFed FASTQs and this seems to be sufficient.@tomwhite I'd begun looking at extending BaseSplitGuesser, but there's enough of a divergence of the fields between the two classes that this is a non-trivial change.