diff --git a/src/BAFpileup.cpp b/src/BAFpileup.cpp
index f0bdfb7..50083c8 100644
--- a/src/BAFpileup.cpp
+++ b/src/BAFpileup.cpp
@@ -211,7 +211,7 @@ void BAFpileup::createBedFileWithChromosomeLengths(std::string bedFileWithRegion
 			name  = strs[0];
 			value = atoi(strs[1].c_str());
 		}
-		if (strs.size()>=3 && strs[0].substr(0,3)!="chr") {
+		if (strs.size()>=3 && strs[0].substr(0,3)!="chr" && !isFai) {
 			name  = strs[1];
 			value = atoi(strs[2].c_str());
 		}
diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp
index 3800f42..36ecc19 100644
--- a/src/GenomeCopyNumber.cpp
+++ b/src/GenomeCopyNumber.cpp
@@ -371,7 +371,7 @@ void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string c
 	cout << normalNumberOfPairs_<< " reads used to compute copy number profile\n";
 	if (normalNumberOfPairs_==0) {
         cerr << "\nError: FREEC was not able to extract reads from " << mateFileName;
-        cerr << "\n\nCheck your parameters: inputFormat and matesOrientation\n";
+        cerr << "\n\nCheck your parameters: inputFormat and mateOrientation\n";
         cerr << "Use \"matesOrientation=0\" if you have single end reads\n";
         cerr << "Check the list of possible input formats at http://bioinfo-out.curie.fr/projects/freec/tutorial.html#CONFIG\n\n";
 
diff --git a/src/freec b/src/freec
index 9885bd8..ec3a903 100644
Binary files a/src/freec and b/src/freec differ
diff --git a/src/main.cpp b/src/main.cpp
index 4424d66..30f804f 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -275,6 +275,8 @@ int main(int argc, char *argv[])
 	std::string sample_MateCopyNumberFile = "";
     string sample_inputFormat = std::string(cf.Value("sample","inputFormat",""));
     std::string sample_mateOrientation = (std::string)cf.Value("sample","mateOrientation","0");
+    sample_mateOrientation = (std::string)cf.Value("sample","matesOrientation",sample_mateOrientation);
+
 
     if (has_sample_MateFile) {
         sample_MateFile = std::string(cf.Value("sample","mateFile")) ;
diff --git a/src/myFunc.cpp b/src/myFunc.cpp
index 4f5a290..3908ab0 100644
--- a/src/myFunc.cpp
+++ b/src/myFunc.cpp
@@ -322,7 +322,7 @@ void readFileWithGenomeInfo(const std::string &chrLenFileName, std::vector<std::
 			name  = strs[0];
 			value = atoi(strs[1].c_str());
 		}
-		if (strs.size()>=3 && strs[0].substr(0,3)!="chr") {
+		if (strs.size()>=3 && strs[0].substr(0,3)!="chr" && !isFai) {
 			name  = strs[1];
 			value = atoi(strs[2].c_str());
 		}
diff --git a/src/version.h b/src/version.h
index 4135a6d..53f88d2 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 = 11.4;
+const double FREEC_VERSION = 11.5;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif