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Add a CRAM file size regression test#1969

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daviesrob merged 1 commit into
samtools:developfrom
jkbonfield:cram-size-test
Jan 25, 2024
Merged

Add a CRAM file size regression test#1969
daviesrob merged 1 commit into
samtools:developfrom
jkbonfield:cram-size-test

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@jkbonfield

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This mainly tests htslib, but it doesn't have a good large general purpose CRAM file for validation. We don't really have a large enough one here either, but this is sufficient.

We could create our own artificial one, but the current test spots the problem in #1968 so it's an easy starting point. Are there zlib, bzip2, or lzma implementations which break this? I tested zlib and libdeflate, and our check is 2% over that so this is a reasonable buffer.

If it breaks, we can amend the testing.

This mainly tests htslib, but it doesn't have a good large general
purpose CRAM file for validation.  We don't really have a large enough
one here either, but this is sufficient.

We could create our own artificial one, but the current test spots the
problem in samtools#1968 so it's an easy starting point.  Are there zlib,
bzip2, or lzma implementations which break this? I tested zlib and
libdeflate, and our check is 2% over that so this is a reasonable
buffer.

If it breaks, we can amend the testing.
@daviesrob daviesrob self-assigned this Jan 23, 2024
@daviesrob daviesrob merged commit a4c77e7 into samtools:develop Jan 25, 2024
daviesrob added a commit to daviesrob/samtools that referenced this pull request Apr 12, 2024
whitwham pushed a commit that referenced this pull request Apr 12, 2024
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2 participants