Re: [Samtools-help] CRAM index files

[Vadim Z. <va...@eb...>]

Hopefully fixed, please try again.

Vadim

On 18/08/2015 09:45, James Bonfield wrote:
> 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
>