Does anyone out there use data in htslib that *isn't* just bgzf wrapped?
I'm working on speeding this up with multi-threading improvements, but
it would be useful to have a better set of tests than simple BAM and
BCF.
The bgzf.c code deals with totally uncompressed data (so not samtools
view -u, but no zlib wrap at all) and also vanilla gzip data.
I don't believe such formats are in use in the wild for BAM and I
don't see any point in using gzip over bgzf for BCF either, but I
don't know much of the use of this library beyond that narrow world.
Tabix is one possibility, but I've no idea what sort of data people
use tabix with. Tabix docs state it must be used on bgzip (bgzf)
data, so I assume the gzip or uncompressed formats are irrelevant to
it.
I can envisage other Z_FULL_FLUSH oriented gzip interfaces that still
permit random access (by something other than bai or csi), but do such
tools exist and are they using htslib? It's possible the gzip code
dates back to razip so if anyone has any background to why this code
exists please illuminate me.
Regards,
James
PS. For what it's worth, there are bugs in the pure gzip handling code
within htslib anyway so I *hope* it's unused!
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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The Wellcome Trust Sanger Institute is operated by Genome Research
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company registered in England with number 2742969, whose registered
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