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Gap V4.3

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue Nov 17 09:25:24 EST 1998

In article <365039CC.946AB327 at nibsc.ac.uk> ajenkins at nibsc.ac.uk writes:
>Is this a bug or a new style.
>We have recently upgraded our Staden software.
>Since the upgrade, when I ask the software to 'Dump Contig To file' it does
>so with a rather large gap between the sequence readings name's and the
>start of the sequence.

The difference is due to increasing the maximum name length from 16 to
32 characters, hence we need to allow for an extra 16 characters in
the dump contig output. This is not a bug, just a side effect of the
change as the printing code automatically works out the size
required. It's not possible at present to change this, however I'll
add it to my todo list. (Basically, I'll probably do the easiest fix
which is to make it adjustable from a .gaprc setting.)

For now, all I can suggest is using the unix cut command to strip out
any unwanted space. Eg having saved output to 'dump.contig', instead
of "lpr dump.contig" try:

	cut -c -20,42- dump.contig | lpr

(You may want to adjust the "20", depending on the length of your
reading names.)

Perhaps the 'correct' approach is to automatically determine the
maximum length of a reading name. However one long name would 'ruin'
the effect.

As always, suggestions are welcome.

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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