[BioRuby] Benchmarking FASTA file parsing

[Naohisa GOTO]

On Sun, 15 Aug 2010 15:19:03 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> > 1. Adjustment of file position.
> > The separator used to read a fasta entry is "\n>", but the ">"
> > should be belonging to the next entry. To adjust this, the last
> > ">" is stored to @entry_overrun. The Bio::FlatFile wrapper will
> > use the content of @entry_overrun in the next time of reading.
> 
> I first thought as such, but I could not find the code that actually
> use it.  Could you specify where it is used?

The "adjustment of file position" have already been replaced by
a constant DELIMITER_OVERRUN. I'm sorry I've forgotten things.

So, currently, only the role of the 2 is expected.

-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org