On Thu, Feb 08, 2018 at 09:32:00AM -0700, Brent Pedersen wrote:
> I've been working more with crams lately and in some cases, it seems
> the default behavior of htslib is to automatically start downloading
> reference files locally even though I have not set REF_CACHE or
> REF_PATH. This is deep in a complex pipeline behind several layers of
> abstraction, but I think this is the default.
If you don't set them it'll automatically default to using the EBI for
REF_PATH and ~/.cache/hts-seqs (IIRC) for REF_CACHE.
If you really wish to totally disable them, keep REF_CACHE clear and
set REF_PATH to somewhere with no files, eg /foo, and it'll fail the
search.
It should then fail.
James
--
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA
--
The Wellcome 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.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
