Hi, I like zero-based indexing, because I am using that (Though there are two half-baked OneIdx, ZeroIdx newtypes buried somewhere) everywhere.
And I feel confident replying because I just noticed that have a use for this library -- thanks ;-) Btw. I would use computer-science indexing (zero-based) internally and only convert to biology indexing in front-ends where needed. Gruss, Christian >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 _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
