//***************************************************************************************************************
int ChimeraSlayer::getChimeras(Sequence* query) {
try {
- if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); printResults.trimQuery = *trimQuery; }
+ if (trimChimera) {
+ trimQuery = new Sequence(query->getName(), query->getAligned());
+ printResults.trimQuery = *trimQuery;
+ }
chimeraFlags = "no";
printResults.flag = "no";
//you must create a template
vector<Sequence*> thisTemplate;
if (templateFileName != "self") { thisTemplate = templateSeqs; }
- else { thisTemplate = getTemplate(query); } //fills thistemplate and creates the databases
+ else { thisTemplate = getTemplate(query); } //fills this template and creates the databases
if (m->control_pressed) { return 0; }
if (m->control_pressed) { return 0; }
string chimeraFlag = maligner.getResults(query, decalc);
+
if (m->control_pressed) { return 0; }
+
vector<results> Results = maligner.getOutput();
- //found in testing realigning only made things worse
if (realign) {
ChimeraReAligner realigner(thisTemplate, match, misMatch);
realigner.reAlign(query, Results);