fixed a bug in calculating the # of ambig bases

diff --git a/sequence.cpp b/sequence.cpp
index 423b9058b23b0815326465f86b9916777c0359ce..e9487c519e0d3e0378266eb537d15e28979546dc 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -75,8 +75,8 @@ void Sequence::initialize(){
        isAligned = 0;
        startPos = -1;
        endPos = -1;
-       longHomoPolymer = 0;
-       ambigBases = 0;
+       longHomoPolymer = -1;
+       ambigBases = -1;
        
 }      
 
@@ -212,7 +212,7 @@ int Sequence::getAlignLength(){
 
 int Sequence::getAmbigBases(){
        if(ambigBases == -1){
-       
+               ambigBases = 0;
                for(int j=0;j<numBases;j++){
                        if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
                                ambigBases++;
@@ -226,8 +226,8 @@ int Sequence::getAmbigBases(){
 //********************************************************************************************************************
 
 int Sequence::getLongHomoPolymer(){
-       if(longHomoPolymer == 0){
-
+       if(longHomoPolymer == -1){
+               longHomoPolymer = 1;
                int homoPolymer = 1;
                for(int j=1;j<numBases;j++){
                        if(unaligned[j] == unaligned[j-1]){