bgzip reindex performance

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#378 opened on May 16, 2016 4 comments 0 reactions 1 assignee View on GitHub

@jkbonfield is already working on this.

Since May 23, 2016.

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This issue has not been assessed yet.

Description

Hi,

I have noticed that bgzip's reindex functionally seem slower that is necessary.

The index in made up of the uncompressed and compressed offsets for each bgzip block in a file possibly excluding the final block. I think all this information is contained within the bgzip header and footer i.e. the BSIZE feild and the ISIZE field (page 11: https://samtools.github.io/hts-specs/SAMv1.pdf)

However the current implementation is passing the entire file block-wize to bgzf_read() in bgzf.c which I think is decompressing the file to rebuild the index.

Is there any reason why the reindexing functionality can be implemented by just seeking through the file and just pulling out the BSIZE and ISIZE fields?

By the way I am interested in reindex performance due to another issued I raised in parallel to this:
https://github.com/samtools/htslib/issues/377

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