Re: [wgs-assembler-users] Erroneous ASM file

[Walenz, B. <bw...@jc...>]

Dang, I think you might have hit a stupid bug I introduced and then fixed
much later than I'm happy to admit.

Broken in this:

r4393 | brianwalenz | 2013-08-24 03:46:56 -0400 (Sat, 24 Aug 2013) | 2 lines
Add runCA option cgwPreserveConsensus.

Fixed in this:

r4406 | brianwalenz | 2013-09-06 18:42:08 -0400 (Fri, 06 Sep 2013) | 3 lines
The cgwPreserveConsensus default value was incorrect resulting in cgw always
retaining the consensus sequence, and 8-consensus never recomputing it.

Does 'svn info' show a revision between those two?



On 9/30/13 8:12 AM, "Mayank Mahajan" <may...@ic...> wrote:

> Hello,
> I have been using the unstable release of WGS assembler. I have some
> really good assemblies as per my post assembly checks.
> The problem is that the {CCO tags in the asm file are all loosing the
> information whenever they have more than one unitig in the contig.
> Whenever there is more than one unitig in the contig the quality
> values of the whole consensus just become zero. The contigs loose all
> the gap information which takes into consideration the indels in the
> reads. And respectively, all the reads also loose the indel
> information in the contigs.
> 
> Regards,
> Mayank Mahajan