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Investigate faster inflate implementations #14

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Arkanosis opened this issue Jun 17, 2018 · 1 comment
Open

Investigate faster inflate implementations #14

Arkanosis opened this issue Jun 17, 2018 · 1 comment
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@Arkanosis
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The currently used inflate implementation works pretty well, but is a lot slower than zlib. This means that unless we use multiple threads, bamrescue is slower than gzip. Switching to a state-of-the-art inflate implementation could make bamrescue as fast as gzip with a single thread, and much faster with multiple threads.

@Arkanosis Arkanosis added this to the v0.4 milestone Jun 17, 2018
@Arkanosis Arkanosis self-assigned this Jun 17, 2018
@Arkanosis
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Update the benchmarks against gzip -t, then, and also add samtools quickcheck. The latter should be faster than both gzip and bamrescue, but only checks for corruption in the header and the footer.

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