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Alignments in the contig editor

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Thu May 18 10:37:12 EST 2000

In <WKz*GMpso at news.chiark.greenend.org.uk> Tim Cutts <timc at chiark.greenend.org.uk> writes:

> I've just been observing some odd behaviour in the contig editor of the
> 1999.1 release (haven't had time to get the new version yet!)
> In one particular contig, the textual alignment of the reads looks
> absolutely fine, but when I open the traces for some reads, they are not
> aligned with each other.

Can you explain this in more detail? (You could email me a screenshot if you

Specifically, we would expect the cursor line in the trace display to match
the cursor position in the contig editor. All the trace display cursor lines
should be aligned to one another. However the rest of the bases (to the left
and right) may not be aligned due to variation in the base spacing. It is not
possible to completely align all the trace that is displayed without having
variable scaling in the X direction (or whatever the trace equivalent of
pads/gaps would be).

Note that we did find a problem where the traces (when brought up from the
consensus) had the cursor line displayed on the correct bases, but did not
have aligned cursor lines. This is a bug triggered when the display attempts
to draw past the end of a trace. This only happens when bringing up new
traces; moving the editor cursor will snap the traces back into alignment.

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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