added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index d877f4b93f33d8123ff6a1a9f7f839dc680fcf61..a359607a3ea11fa118efed129407ee608d4903e5 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -603,7 +603,7 @@ int Sequence::getLongHomoPolymer(){
 int Sequence::getStartPos(){
        if(startPos == -1){
                for(int j = 0; j < alignmentLength; j++) {
-                       if(aligned[j] != '.'){
+                       if((aligned[j] != '.')&&(aligned[j] != '-')){
                                startPos = j + 1;
                                break;
                        }
@@ -668,7 +668,7 @@ int Sequence::filterFromPos(int end){
 int Sequence::getEndPos(){
        if(endPos == -1){
                for(int j=alignmentLength-1;j>=0;j--){
-                       if(aligned[j] != '.'){
+                       if((aligned[j] != '.')&&(aligned[j] != '-')){
                                endPos = j + 1;
                                break;
                        }
@@ -682,7 +682,7 @@ int Sequence::getEndPos(){
 //********************************************************************************************************************
 
 void Sequence::padFromPos(int end){
-       cout << end << '\t' << endPos << endl;
+       //cout << end << '\t' << endPos << endl;
        for(int j = end; j < endPos; j++) {
                aligned[j] = '.';
        }