extract_readings quality function not working....

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Tue Aug 14 04:28:28 EST 2001


In <3B72C557.7AB05810 at genome.wi.mit.edu> major at genome.wi.mit.edu (major) writes:

> Here is the piece of code(which works spledidly with Staden.02_97.beta,
> except for the filename char limit...)
> 
[...]

> if {$specdir} {
>     extract_readings -io $io -readings $all_reads -quality 1 -directory $dirname


Try using -format 2 instead. Formats 0, 1 and 2 correspond to the GUI; normal, 
preassembled, directed assembly.

Sorry about the programming documentation being out of date. I'd expect there
to be heaps of other changes since it was written (1997) too. Unfortunately
it's hard to find the time, but we really ought to update this stuff. It's
just such a _tedious_ effort. Maybe I should investigate some auto-generation
mechanism to extract comments from the source.

James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/




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