On Fri, Apr 06, 2001 at 05:24:40PM +1200, Schreiber, Mark wrote:
> The SimpleAssembly test seems to be failing, I get the following output:
>
> gattacannnnnnnnnnnnn
> g
> gatta
> ttacann
> ttacannnn
> tcg
> nnnn
> fragment at 1-7
> test at 2-3
> fragment at 10-13
> test at 9-10
> sub-test at 9-9
>
> I am thinking all those n's shouldn't be there (at least some of them
> anyhow)
Nope, you're right -- there was a fairly subtle bug in the
seqString/subStr optimized implementations in AssembledSymbolList.
Only really affected very short assemblies, for the most part
(which is how it went un-noticed for so long).
Hope this is fixed now -- if you still see any more problems,
AssembledSymbolList.locationUpstreamOfPoint is probably
prime suspect...
Thomas.
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