thanks for the quick fix. On Thu, May 11, 2017 at 3:24 AM, James Bonfield <j...@sanger.ac.uk> wrote: > 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.
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