//***************************************************************************************************************
ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div,
-int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
+int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas) : Chimera() {
try {
fastafile = file;
templateFileName = temp; templateSeqs = readSeqs(temp);
realign = r;
trimChimera = trim;
numNoParents = 0;
+ blastlocation = blas;
doPrep();
}
//***************************************************************************************************************
//template=self
ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div,
- int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
+ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas) : Chimera() {
try {
fastafile = file; templateSeqs = readSeqs(fastafile);
templateFileName = temp;
trimChimera = trim;
priority = prior;
numNoParents = 0;
+ blastlocation = blas;
createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
}else if (searchMethod == "blast") {
//generate blastdb
- databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
+ databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation);
if (m->control_pressed) { return 0; }
}else if (searchMethod == "blast") {
//generate blastdb
- databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+ databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation);
if (m->control_pressed) { return userTemplate; }