Re: [Samtools-devel] Indexing a BAM Index (BAI)

[James B. <jk...@sa...>]

On Mon, Nov 10, 2014 at 03:55:44PM +0000, Vadim Zalunin wrote:
> Index file size for a CRAM file should be smaller than for a 
> corresponding BAM file because each container/slice is used as a 
> contiguous read, leaving the rest to the iterators. This is equivalent 
> to indexing every 10k (by default) reads as one long read. I wonder if 
> reduced resolution could be used for BAM files as well. This should not 
> affect readers if I'm not mistaken.

We discussed this at our weekly meeting today and concluded that
skipping some bins from indexing is a comparable thing and possibly
not that hard to do, but we are unsure of whether it is necessary.

CSI has a variety of options controlling granularity already, so
perhaps just exposing these to the user is sufficient. Plus it is
already a lot smaller than BAI anyway due to compression.

James

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