v11.0 - added mistake-proofing for the step parameter

Author: valeu

src/freec

@@ -816,13 +816,20 @@ int main(int argc, char *argv[])
 
 
     if (WESanalysis == false)    {
-        if (step != NA) {
-            sampleCopyNumber.setStep(step);
-        }
         if (has_sample_mateCopyNumberFile) {
             sampleCopyNumber.readCopyNumber(sample_MateCopyNumberFile);
-            step = sampleCopyNumber.getStep();
+            int step_fromProfile = sampleCopyNumber.getStep();
+            if (step!= NA && step_fromProfile !=step) {
+                cerr << "Error: according to " << sample_MateCopyNumberFile<< " your step paramter is equal to step_fromProfile\n";
+                cerr << "However, you set step=" <<step<< " in your config file\n";
+                cerr << "This created this error. Either delete \"step\" from your config or set it to the right value of "<<sample_MateCopyNumberFile<<"\n";
+                exit (-1);
+            }
+            step=step_fromProfile;
         } else {
+            if (step != NA) {
+                sampleCopyNumber.setStep(step);
+            }
             if (!sample_copyNumber_pileup_read && has_window) {
                     sampleCopyNumber.readCopyNumber(sample_MateFile, sample_inputFormat, sample_mateOrientation,chrLenFile, window, step);
             } else if (!sample_copyNumber_pileup_read && !has_window) {

src/main.cpp

@@ -2617,8 +2617,9 @@ MateOrientation getMateOrientation(std::string const& matesOrientation)
   if (matesOrientation.compare("FF") == 0 || matesOrientation.compare("RR") == 0 || matesOrientation.compare("FF/RR") == 0 || matesOrientation.compare("RR/FF") == 0) {
 	return SOLID_MATE_PAIRS;
   }
-
-  return UNKNOWN_MATE_ORIENTATION;
+  cerr << "Error: you have set an unknown read orientation: \""<<matesOrientation<<"\" ; it does not match 0, RF, FR or FF; please correct your config file.\n";
+  exit(1);
+  return SINGLE_END_SORTED_SAM; // instead of UNKNOWN_MATE_ORIENTATION;
 }
 
 InputFormat getInputFormat(std::string const& inputFormat)

src/myFunc.cpp

@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 10.9;
+const double FREEC_VERSION = 11.0;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif