alignLength = referenceSeqs[0].length();
- chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents";
+ chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
// chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
}
int lDiffs = 0;
for(int l=0;l<alignLength;l++){
- if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
lDiffs++;
}
left[i][l] = lDiffs;
int rDiffs = 0;
int index = 0;
for(int l=alignLength-1;l>=0;l--){
- if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
rDiffs++;
}
right[i][index++] = rDiffs;
int mismatch = 0;
for(int i=0;i<alignLength;i++){
- if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
+// if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
+ if(chimeraRefSeq[i] != '.'){
if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){ /* do nothing */ }
else if(querySeq[i] == chimeraRefSeq[i]){
match++;