On Fri, Feb 13, 2015 at 1:55 PM, Stefan Nordlander <stefan.o.nordlan...@gmail.com> wrote: > Greetings samtools-list members, > > I'm assisting an associate with some calculations, and we've run into some > problems with samtools. > What I'm trying to do is to generate a .bai index file but I get the > following error message: > > NO_COOR reads not in a single block at the end 0 -1
If your BAM file is sorted, then all the reads with no POS value (i.e. NO_COOR) should be at the end. Are they? > I found the suggestion to add -c to samtools which did not help. I also > found at http://sourceforge.net/p/samtools/mailman/message/33155863/ the > suggestion that samtools only supports chromosome length of 512Mbp for index > generation. However our longest chromosome is +248Mbp, far from 512Mbp. > > Any help would be appreciated! Yes, this does not look like a problem with the reference length. Peter ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
