[Biopython] Bio.SeqIO.index() - gzip support and/or index stored on disk?

[Kevin Lam]

Just thinking out loud.
would generating a fake region id (unique for each read id) and the
corresponding index when creating the bam be a good quick fix to utilise bam
format for ID based retrieval?
Or would the double mapping slow things down considerably?
Kevin

>
> What do you think about co-opting the SAM/BAM format for this? This
> would make it more specific for things that can go into BAM (so no
> GenBank and what not), but would have the advantage of working with
> existing workflows.
>
> Region based indexing is already implemented for BAM, but it would
> be really useful to also have ID based retrieval along the lines of
> what you are proposing.
>
> Brad
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