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@jmarshall jmarshall commented Nov 26, 2025

This is a draft PR adding some functions to pack and unpack the SEQ and QUAL fields individually, enabling third-party code to take advantage of the optimised and SIMD-optimized implementations of this functionality that HTSlib provides.

The format ones were the motivation for this; in particular they will be immediately useful for pysam. The parse ones are perhaps of less widespread use (at least in their current form) as usually if writing to a bam1_t there’ll need to be some memory reallocating going on too. But I think pysam would benefit from accessing HTSlib’s implementations of these too.

I hoped to have this a little bit less draft than this sooner, but here’s the basic idea and implementation for your perusal.

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