-string ChopSeqsCommand::getChoppedUnaligned(Sequence seq) {
- try {
- string temp = seq.getUnaligned();
-
- //if needed trim sequence
- if (end != 0) {
- if (temp.length() > end) { temp = temp.substr(0, end); }
- else { temp = ""; }
- }else { //you are using fromend
- if (temp.length() > fromend) { temp = temp.substr(0, (temp.length()-fromend)); }
- else { temp = ""; } //sequence too short
- }
-
- return temp;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ChopSeqsCommand::getChoppedAligned(Sequence seq) {