v11.2: better fit of GC-content bias in contaminated samples

valeu · valeu · commit ec1917dfd31f · 2018-01-23T19:38:10.000+01:00
diff --git a/src/freec b/src/freec
diff --git a/src/myFunc.cpp b/src/myFunc.cpp
@@ -1497,7 +1497,7 @@ std::string stringFromBool (bool value) {
 }
 
 float runEM (const vector<float>& x,const vector<float>& y,double * a, int degree, int & NumberOfIterations,int ploidy, int maximalNumberOfCopies, bool intercept, float contamination) {
-
+    if (contamination==0) contamination=0.3; //starting from v11.2 - to improve the fit
 	float rmserror = -1;
 
 	if (x.size() != y.size()) {
diff --git a/src/version.h b/src/version.h
@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 11.1;
+const double FREEC_VERSION = 11.2;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif

Original file line number	Diff line number	Diff line change
`@@ -1497,7 +1497,7 @@ std::string stringFromBool (bool value) {`
`1497`	`1497`	`}`
`1498`	`1498`
`1499`	`1499`	`float runEM (const vector<float>& x,const vector<float>& y,double * a, int degree, int & NumberOfIterations,int ploidy, int maximalNumberOfCopies, bool intercept, float contamination) {`
`1500`		`-`
	`1500`	`+ if (contamination==0) contamination=0.3; //starting from v11.2 - to improve the fit`
`1501`	`1501`	`float rmserror = -1;`
`1502`	`1502`
`1503`	`1503`	`if (x.size() != y.size()) {`