Systematically test the GKL deflater/inflater with long reads data about gkl HOT 7 CLOSED

Tentative testing plan: run several roundtrip full-scale tests in which we read in every record in a long reads bam file using the inflater to decompress, and write out a new bam using the deflater to re-compress. Then check the new bam against the original to make sure they're the same once uncompressed.

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@jonn suggested that we also test long reads data with the accelerated SmithWaterman implementation in the GKL, just to see if it can handle long reads.

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I collected several test files with long reads and sent over some signed URLs for testing on 5/1. I'm keeping them around if other folks need access (just let me know).

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@Kmannth has confirmed that they've received the long reads test data @jonn-smith sent them.

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@droazen , should I test GATK 4.2.* with our long reads data, given that these releases may have the relevant patches?

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@SHuang-Broad 4.2.1 was the first GATK release with the new GKL. Any feedback you could provide on how the new GKL performs on long reads data would be extremely welcome!

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We tested Long Reads data form @jonn-smith with our latest release. If there is an issue please reopen this bug.

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