[Denovoassembler-devel] [PATCH] clean up / simplify CoverageDistribution function

[David E. (gringer) <dav...@mp...>]

I've been trying to clean up the coverage distribution function to make 
it easier for me to understand.

Using this patch, it works with my simulated phiX data (because of the 
fallback to max coverage with no votes -- it looked like this was in the 
code before?).

However, it fails for the S.med 454 data (transcriptome data, in which 
coverage values decrease sharply from the start). I noticed that I can 
'fix' the peak finding code by making this change (about line 83):

if((votes[i] > votes[largestPosition])
->
if((votes[i] >= votes[largestPosition])

But then the minimum position is set to the largest position, and the 
assembler panics. I need to set the minimum coverage to the coverage at 
the first position for things to work with that data:

m_minimumCoverage=x[0]; // about line 98

I haven't put these additional changes in the patch, because I'm not 
sure how they will affect other things... and [as I've just noticed] I 
get a segfault on the 454 data with my code when doing this.... I'll try 
to nail that down in the next day or so.

-- David