[Bioperl-guts-l] [Bug 2063] Bio::DB::Fasta fails to index files over 4GB

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Mon Aug 7 15:34:54 EDT 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2063





------- Comment #1 from charles.tilford at bms.com  2006-08-07 15:34 -------
Created an attachment (id=408)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=408&action=view)
Patch against v1.44

Patched against: Fasta.pm,v 1.44 2006/07/17 10:39:37 sendu
The problem exists in any version which uses 'NNnnCa*' as the pack format
(starts from v1.1 AFAIK).

Two pack formats are defined as constants - I assume there is a performance
advantage to having the code compile with a constant pack format.

If none of the files being indexed are greater than 4GB (as determined by the
-s flag), then 'NNnnCa*' is used both to pack and unpack; this should provide
backwards compatibility with existing indices. Otherwise, 'QQnnCa*' is used to
pack both the offset and sequence length as 64-bit ints. Bifurcation is done
using different method references for packing and unpacking.

I have tested this against single files, but not against a directory. The code
*should* work on a directory as well, and will use 64-bit packing if *any* file
in the directory exceeds 4GB.


-- 
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.


More information about the Bioperl-guts-l mailing list