bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
try {
string rawSequence = seq.getUnaligned();
- int seqLength = rawSequence.length();
- string name;
+ int seqLength; // = rawSequence.length();
+ string name, temp, temp2;
- qFile >> name;
+ qFile >> name >> temp;
+
+ splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
+ convert(temp, seqLength); //converts string to int
+
if (name.length() != 0) { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); } }
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }