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Advanced rescue of correctable corruptions #13

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Arkanosis opened this issue Jun 4, 2018 · 0 comments

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Arkanosis commented Jun 4, 2018

Some corruptions are actually reliably correctable without too much computation:

if fixed header bytes are incorrect, they can be fixed as long as the CRC32 properly validates the payload (100% reliable as long as the bam usage is concerned);
if the payload size is incorrect, it can be fixed as the CRC32 already validates the payload (100% reliable);
if there's a deflate or CRC32 error and the next block is shifted, try to fix the bgzf data size (100% reliable if it works).

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Rescue corrupted bam files #3

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