v10.5 - check for sorted BED

BoevaLab · Mar 17, 2017 · f41a414 · f41a414
1 parent bae2244
commit f41a414
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Showing 5 changed files with 11 additions and 78 deletions.
diff --git a/src/ChrCopyNumber.cpp b/src/ChrCopyNumber.cpp
@@ -1458,6 +1458,16 @@ void ChrCopyNumber::fillCGprofile(std::string const& chrFolder) {
                     //count = end;
                     //and delete prefix in text;
                     int howMuchToDelete = nextStart - start;
+                    if (howMuchToDelete<0) {
+                        cerr << "Error: your BED file with coordinates of targeted regions does not seem to be sorted\nCheck chromosome "<<chromosome_<<"\n";
+                        cout << "Exit Control-FREEC: before reruning, please, sort the BED file with coordinates of the targeted regions\n";
+                        exit(-1);
+                    }
+                    if (howMuchToDelete==0) {
+                        cerr << "Error: your BED file with coordinates of targeted regions may contain duplicates\nCheck chromosome "<<chromosome_<<"\n";
+                        cout << "Exit Control-FREEC: before reruning sort the BED file with coordinates of the targeted regions and REMOVE DUPLICATED REGIONS\n";
+                        exit(-1);
+                    }
                     text = text.substr(howMuchToDelete);
 			    } else {
                     text = "";

diff --git a/src/RSSerror.cpp b/src/RSSerror.cpp
diff --git a/src/RSSerror.h b/src/RSSerror.h
diff --git a/src/freec b/src/freec
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 = 10.4;
+const double FREEC_VERSION = 10.5;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif