On Mar 28, 2011, at 9:14 AM, Ketil Malde wrote: > Nick Ingolia <n...@ingolia.org> writes: > > Another thing - I noticed you used zero-based indices. I've been using > 1-based ones (lately, can't vouch entirely for the old stuff), since > that's what the tools I used tended to produce. > > This is one of those endian things, it doesn't matter much one way or > another, but perhaps we should agree on a single standard, and try to > make everything consistent?
I'm pretty strongly in favor of 0-based indexing, because 0) it's consistent with 0-based indexing of string-like data types and vectors, 1) it's consistent with the samtools C library (I have bindings for this library that I'm cleaning up for release son), and 2) it's consistent with BED format annotation files, which I prefer because among other things they have one line per annotation. I do know that 1-based indices are common among biologists--but they also often skip zero entirely, which is pretty unworkable for a library interface. If you're committed to 1-based indices, we could exploit the newtype wrapper around Offset to provide an interface with 1-based offsets. Best, --Nick _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
