- // string constants
- static const string SPLIT_MAPPED_TOKEN = ".MAPPED";
- static const string SPLIT_UNMAPPED_TOKEN = ".UNMAPPED";
- static const string SPLIT_PAIRED_TOKEN = ".PAIRED_END";
- static const string SPLIT_SINGLE_TOKEN = ".SINGLE_END";
- static const string SPLIT_REFERENCE_TOKEN = ".REF_";
-
- string GetTimestampString(void) {
-
- // get human readable timestamp
- time_t currentTime;
- time(¤tTime);
- stringstream timeStream("");
- timeStream << ctime(¤tTime);
-
- // convert whitespace to '_'
- string timeString = timeStream.str();
- size_t found = timeString.find(" ");
- while (found != string::npos) {
- timeString.replace(found, 1, "_");
- found = timeString.find(" ", found+1);
- }
- return timeString;
- }
-
- // remove copy of filename without extension
- // (so /path/to/file.txt becomes /path/to/file )
- string RemoveFilenameExtension(const string& filename) {
- size_t found = filename.rfind(".");
- return filename.substr(0, found);
+// string constants
+static const string SPLIT_MAPPED_TOKEN = ".MAPPED";
+static const string SPLIT_UNMAPPED_TOKEN = ".UNMAPPED";
+static const string SPLIT_PAIRED_TOKEN = ".PAIRED_END";
+static const string SPLIT_SINGLE_TOKEN = ".SINGLE_END";
+static const string SPLIT_REFERENCE_TOKEN = ".REF_";
+
+string GetTimestampString(void) {
+
+ // get human readable timestamp
+ time_t currentTime;
+ time(¤tTime);
+ stringstream timeStream("");
+ timeStream << ctime(¤tTime);
+
+ // convert whitespace to '_'
+ string timeString = timeStream.str();
+ size_t found = timeString.find(" ");
+ while (found != string::npos) {
+ timeString.replace(found, 1, "_");
+ found = timeString.find(" ", found+1);