From 30f81aa94ec6cba6bb972a59b13b66d14a281185 Mon Sep 17 00:00:00 2001
From: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: Wed, 13 Feb 2019 22:04:28 +0100
Subject: [PATCH 1/2] Improve slightly procedure for best ploidy detection

---
 src/main.cpp | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/main.cpp b/src/main.cpp
index 30f804f..369cb9a 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -1009,17 +1009,40 @@ int main(int argc, char *argv[])
     int secondBest= ploidies[max_element(percentage_GenExpl.begin(),percentage_GenExpl.end())-percentage_GenExpl.begin()];
     cout << "..Best ploidy could have been set to "<<secondBest << " according to the percentage of the copy number changes explained by a model with a given ploidy"<<endl;
 
+    /*
+    So far null ploidy was reset from 4 to 2 if fraction of genome explained in case of
+    ploidy = 2 was higher, equal or only slightly lower compared to ploidy = 4 case.
+    In detail, the difference between fractions must have been < 0.05
+
+    Here the 'genomeExplainedMaxDiff' config parameter is introduced to let the user decide.
+    The default value for the param is 0.05
+    */
+    double genomeExplainedMaxDiff = (double)cf.Value("general", "genomeExplainedMaxDiff", 0.05);
+    cout << "..genomeExplanedMaxDiff set to: "<<genomeExplainedMaxDiff << "."<<endl;
+
     if (bestPloidy==4 && std::find(ploidies.begin(), ploidies.end(), 2) != ploidies.end()) {
         int ind2=std::find(ploidies.begin(), ploidies.end(), 2)-ploidies.begin();
         int ind4=std::find(ploidies.begin(), ploidies.end(), 4)-ploidies.begin();
 
-        if (percentage_GenExpl[ind4]-percentage_GenExpl[ind2]<0.05 || unexplainedChromosomes[ind2]<=1) {
+        if (percentage_GenExpl[ind4]-percentage_GenExpl[ind2]<genomeExplainedMaxDiff || unexplainedChromosomes[ind2]<=1) {
             bestPloidy=2;
             cout << "..Changed ploidy to 2 as there is little difference in the fit betweeen ploidies 4 and 2:" << endl;
             cout << "unexplained regions for ploidy 2 are located on " <<unexplainedChromosomes[ind2]<< " chromosomes"<< endl;
         }
     }
 
+    // Add also scenario 3 => 2 for best ploidy. Use same rules  as in case of 4 => 2 change
+    if (bestPloidy==3 && std::find(ploidies.begin(), ploidies.end(), 2) != ploidies.end()) {
+        int ind2=std::find(ploidies.begin(), ploidies.end(), 2)-ploidies.begin();
+        int ind3=std::find(ploidies.begin(), ploidies.end(), 3)-ploidies.begin();
+
+        if (percentage_GenExpl[ind3]-percentage_GenExpl[ind2]<genomeExplainedMaxDiff || unexplainedChromosomes[ind2]<=1) {
+            bestPloidy=2;
+            cout << "..Changed ploidy to 2 as there is little difference in the fit betweeen ploidies 3 and 2:" << endl;
+            cout << "unexplained regions for ploidy 2 are located on " <<unexplainedChromosomes[ind2]<< " chromosomes"<< endl;
+        }
+    }
+
 
 
     if (bestPloidy!=ploidies.back()) {

From ef2113e8b5f6ad35aa90e848e799235cb824bbdf Mon Sep 17 00:00:00 2001
From: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: Wed, 13 Feb 2019 22:43:55 +0100
Subject: [PATCH 2/2] Bump version

---
 src/version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/version.h b/src/version.h
index 53f88d2..727c5c1 100644
--- a/src/version.h
+++ b/src/version.h
@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 11.5;
+const double FREEC_VERSION = 11.6;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif