if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
if(!success) { trashCode += 'q'; }
- qFile.close();
}
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
outFASTA.close();
scrapFASTA.close();
outGroups.close();
+ if(qFileName != "") { qFile.close(); }
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i]->close();
string name;
qFile >> name;
- if (name.length() != 0) { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); } }
+ if (name[0] == '>') { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine(); } }
+
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
float score;
average += score;
}
average /= seqLength;
-
+
if(average >= qAverage) { success = 1; }
else { success = 0; }
}
//***************************************************************************************************************
-
-