On Wed, May 10, 2017 at 11:34:46AM -0600, Brent Pedersen wrote: > I have a .crai with a negative alignment span. The row looks like this: > > 2225 1 -2147483648 14896634174 936 628560 > > I'm wondering what that means. It was created with samtools 1.3.1
I've now fixed this in htslib and io_lib(scramble). The difference is a tiny one-line change so you can just apply it manually to your source file if you wish. https://github.com/samtools/htslib/commit/a58cd8547526a3be537064639572ff767298326d @@ -482,7 +482,7 @@ static int cram_index_build_multiref(cram_fd *fd, ref = s->crecs[i].ref_id; ref_start = s->crecs[i].apos; - ref_end = INT_MIN; + ref_end = s->crecs[i].aend; } if (ref != -2) { Thanks, James -- James Bonfield (j...@sanger.ac.uk) | 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. ------------------------------------------------------------------------------ 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
