IMO, we should revert these -u options to the old behavior. They break compatibility with other tools and older samtools and adds little benefit.
Heng On Feb 12, 2015, at 7:37, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Wed, Feb 11, 2015 at 1:12 PM, Sendu Bala <s...@sanger.ac.uk> wrote: >> I'm using the latest samtools (1.1) and picard (1.128). >> >> If I make a bam using the -u option of eg. calmd, it now creates >> a raw uncompressed bam (as opposed to a bgzip bam with >> compression level 0, which is what samtools v0 did). >> >> Picard falls over given such a bam: > > This does sound like an unintended regression in samtools. > > I doubt indexing would work on these "naked" BAM files > (with their blocked gzipped wrapper removed) either. > > 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 ------------------------------------------------------------------------------ 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
