Re: [Samtools-help] CRAM index files

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

On Mon, Aug 17, 2015 at 04:16:59PM +0100, Vadim Zalunin wrote:
> Do you have the numbers from Picard's ViewSam? Right now cramtools
> has it's own methods for random access but I'm thinking to switch it
> to htsjdk completely.

After a rather uphill struggling getting a region into ViewSam (why is
this so challenging) I finally got 4 sequences out again for the
1:100000000-100000000 region.

However it appears to work even without an index at all, so I think
ViewSam doesn't support random access and is just streaming.  Is there
a way to make it do random access in the same way that samtools will?
It looks like picard interval-lists work the same way as samtools view
-l and a bed file, rather than as a region query.

James

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https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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