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 -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
