Remove cram seek ability to do range queries via SEEK_CUR.#1878
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daviesrob merged 1 commit intosamtools:developfrom Jan 27, 2025
Merged
Remove cram seek ability to do range queries via SEEK_CUR.#1878daviesrob merged 1 commit intosamtools:developfrom
daviesrob merged 1 commit intosamtools:developfrom
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daviesrob
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Jan 27, 2025
This was a feature that came all the way from the initial index support added to io_lib, but I think it's a misfeature. The consequence of it is on failing with a SEEK_SET (eg network error, or file corruption) it falls back to doing a read-and-discard loop to simulate the seek via SEEK_CUR. This may perhaps be of use when querying stdin, but it's highly unlikely for us to be doing that while also having an index on disk and it's not something we support with other formats. Fixes samtools#1877
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This was a feature that came all the way from the initial index support added to io_lib, but I think it's a misfeature. The consequence of it is on failing with a SEEK_SET (eg network error, or file corruption) it falls back to doing a read-and-discard loop to simulate the seek via SEEK_CUR.
This may perhaps be of use when querying stdin, but it's highly unlikely for us to be doing that while also having an index on disk and it's not something we support with other formats.
Fixes #1877