//**********************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(){
try {
//**********************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(){
try {
vector<string> tempOutNames;
outputTypes["error.summary"] = tempOutNames;
outputTypes["error.seq"] = tempOutNames;
vector<string> tempOutNames;
outputTypes["error.summary"] = tempOutNames;
outputTypes["error.seq"] = tempOutNames;
string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
m->openOutputFile(errorSummaryFileName, errorSummaryFile);
string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
m->openOutputFile(errorSummaryFileName, errorSummaryFile);
if(!ignoreSeq){
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
if(!ignoreSeq){
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);