On Wed, Nov 28, 2018 at 01:24:55AM +0000, Alexander Brown wrote: > The search order to obtain a reference is: > > Use any local file specified by the command line options (eg -T). > > Look for MD5 via REF_CACHE environment variable. > > Look for MD5 in each element of the REF_PATH environment variable. > > Look for a local file listed in the UR: header tag." > > I assume what happened is my "-T fasta" was wrong and so it looked elsewhere > and found the correct file. Is there a way to get an output notifying that > the -T fasta has been skipped? While it worked this time, it's important to > know when this is happening.
That's an interesting idea and I'll look to see how viable this is. Note the search order specified is *per reference*. Thus you can give it a partial reference and it'll use the records listed there and other references from elsewhere. That was by design, but I'm not entirely sure it's useful design! As you indicate, it may be more useful to warn the user that the reference given is incomplete. For what it's worth, it will work still as the MD5sum will be whatever was used (either -T ref.fa or some other route) and stored in the CRAM header. Well I hope so anyway! (Maybe I should batter it with all the corner cases to double check.) 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. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
