[Biopython-dev] [Bug 2837] Reading Roche 454 SFF sequence read files in Bio.SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2837





------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2009-09-04 06:54 EST -------
The Staden IO lib has references to ".srt1.00" (454 sorted v1.00) and also
another SFF index format, which start ".hsh1.00" (hash table v1.00).

See files io_lib/progs/hash_sff.c and io_lib/open_trace_file.c from
http://sourceforge.net/projects/staden/

Scanning their code also confirms my base 255 deduction for the ".srt" indexes,
see function getuint4_255, and the use of 0xFF as a break character.
Interestingly they only expect 4 bytes for the offset (limiting this to almost
4GB SFF files). There is a fifth byte which is usually null, this could be a
name terminator (although this is not actually needed), or used for 4GB+ SFF
offsets.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.