On 01.03.2014 18:48, David Eccles (gringer) wrote:
> I'll try again with a larger kmer size. I guess that might cause a few more
> of those reads to become unique.
Still no luck with k=31.
Patch to only start counting from first valley is attached. I have not yet
tested it, so expect bugs.
- David
diff --git a/code/CoverageGatherer/CoverageDistribution.cpp b/code/CoverageGatherer/CoverageDistribution.cpp
index 90814f9..d906011 100644
--- a/code/CoverageGatherer/CoverageDistribution.cpp
+++ b/code/CoverageGatherer/CoverageDistribution.cpp
@@ -59,9 +59,21 @@ CoverageDistribution::CoverageDistribution(map<CoverageDepth,LargeCount>*distrib
CoverageDepth maximumX=65535-1;
CoverageDepth safeThreshold=256;
+ /** ignore counts prior to first valley */
+ int covStart = 0;
+ LargeCount lastCov = y.at(0); // note: assumes at least one value
+ for(int i=0;i<(int)x.size();i++){
+ if(y.at(i) <= lastCov){
+ covStart = i;
+ lastCov = y.at(i);
+ } else {
+ break;
+ }
+ }
+
/** get the votes to find the peak */
map<int,int> votes;
- for(int i=0;i<(int)x.size();i++){
+ for(int i=covStart;i<(int)x.size();i++){
int largestPosition=i;
for(int j=0;j<windowSize;j++){
int position=i+j;
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