virtual void setDivR(float d) { divR = d; }
virtual void setParents(int p) { parents = p; }
virtual void setMinSim(int s) { minSim = s; }
+ virtual void setPrint(int p) { printAll = p; }
virtual void setCons(string){};
protected:
- bool filter, correction, svg;
+ bool filter, correction, svg, printAll;
int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents;
float divR;
string seqMask, quanfile, filterString, name;
else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents" };
+ string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "printall" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
correction = isTrue(temp);
+ temp = validParameter.validFile(parameters, "printall", false); if (temp == "not found") { temp = "F"; }
+ printAll = isTrue(temp);
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
chimera->setDivR(divR);
chimera->setParents(parents);
chimera->setMinSim(minSimilarity);
+ chimera->setPrint(printAll);
//find chimeras
bool abort;
string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile;
- bool filter, correction, svg;
+ bool filter, correction, svg, printAll;
int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity;
float divR;
Chimera* chimera;
//***************************************************************************************************************
void ChimeraSlayer::print(ostream& out) {
try {
-
mothurOutEndLine();
+ for (int i = 0; i < querySeqs.size(); i++) {
+
+ if (chimeraFlags[i] == "yes") {
+ mothurOut(querySeqs[i]->getName() + "\tyes"); mothurOutEndLine();
+
+ }else{
+ out << querySeqs[i]->getName() << "\tno" << endl;
+ mothurOut("no");
+ }
+ }
+/*
+
+ my $div_ratio_QLA_QRB = $data_struct->{div_ratio_QLA_QRB};
+ my $div_ratio_QRA_QLB = $data_struct->{div_ratio_QLB_QRA};
+
+ my $per_id_QLA = $data_struct->{per_id_QLA};
+ my $per_id_QRB = $data_struct->{per_id_QRB};
+ my $per_id_AB = $data_struct->{per_id_AB};
+ my $per_id_QA = $data_struct->{per_id_QA};
+ my $per_id_QB = $data_struct->{per_id_QB};
+ my $per_id_LAB = $data_struct->{per_id_LAB};
+ my $per_id_RAB = $data_struct->{per_id_RAB};
+ my $per_id_QRA = $data_struct->{per_id_QRA};
+ my $per_id_QLB = $data_struct->{per_id_QLB};
+ my $per_id_QLB_QRA = $data_struct->{per_id_QLB_QRA};
+ my $per_id_QLA_QRB = $data_struct->{per_id_QLA_QRB};
+
+ my $win_left_end5 = $data_struct->{win_left_end5};
+ my $win_left_end3 = $data_struct->{win_left_end3};
+ my $win_right_end5 = $data_struct->{win_right_end5};
+ my $win_right_end3 = $data_struct->{win_right_end3};
+ my $Q = $data_struct->{query_alignment};
+ my $A = $data_struct->{parent_A_alignment};
+ my $B = $data_struct->{parent_B_alignment};
+ my $BS_A = $data_struct->{BS_A};
+ my $BS_B = $data_struct->{BS_B};
+
+ my @Q_chars = @{$Q->{align}};
+ my @A_chars = @{$A->{align}};
+ my @B_chars = @{$B->{align}};
+
+ my $query_acc = $Q->{acc};
+ my $A_acc = $A->{acc};
+ my $B_acc = $B->{acc};
+
+ my $break_left = $Q->{seqPos}->[$win_left_end3];
+ my $break_right = $Q->{seqPos}->[$win_right_end5];
+
+
+ cout << "//\n## CHIMERA\t" << querySeqs[i]->getName() << "\t" << $break_left-$break_right" << endl
+ << "\tDIV_QLARB: ". sprintf("%.3f", $div_ratio_QLA_QRB)
+ << "\tBS_QLARB: " . sprintf("%.2f", $BS_A)
+ << "\tDIV_QRALB: " . sprintf("%.3f", $div_ratio_QRA_QLB)
+ << "\tBS_QRALB: " . sprintf("%.2f", $BS_B)
+ << "\t$A_acc\t$B_acc"
+ << "\tbreakpoint: $break_left-$break_right\n\n";
+
+ ## draw illustration:
+
+ print " Per_id parents: " . sprintf("%.2f", $per_id_AB) . "\n\n";
+ print " Per_id(Q,A): " . sprintf("%.2f", $per_id_QA) . "\n";
+ print "--------------------------------------------------- A: $A_acc\n"
+ . " " . sprintf("%.2f", $per_id_QLA) . " " . sprintf("%.2f", $per_id_QRA) . "\n"
+ . "~~~~~~~~~~~~~~~~~~~~~~~~\\ /~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
+ . "DivR: " . sprintf("%.3f", $div_ratio_QLA_QRB) . " BS: " . sprintf("%.2f", $BS_A) . " |\n"
+ . "Per_id(QLA,QRB): " . sprintf("%.2f", $per_id_QLA_QRB) . " |\n"
+ . " |\n"
+ . " (L-AB: " . sprintf("%.2f", $per_id_LAB) . ") | (R-AB: " . sprintf("%.2f", $per_id_RAB) . ")\n"
+ . " WinL:$win_left_end5-$win_left_end3 | WinR:$win_right_end5-$win_right_end3\n"
+ . " |\n"
+ . "Per_id(QLB,QRA): " . sprintf("%.2f", $per_id_QLB_QRA) . " |\n"
+ . "DivR: " . sprintf("%.3f", $div_ratio_QRA_QLB) . " BS: " . sprintf("%.2f", $BS_B) . " |\n"
+ . "~~~~~~~~~~~~~~~~~~~~~~~~/ \\~~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
+ . " " . sprintf("%.2f", $per_id_QLB) . " " . sprintf("%.2f", $per_id_QRB) . "\n"
+ . "---------------------------------------------------- B: $B_acc\n";
+ print " Per_id(Q,B): ". sprintf("%.2f", $per_id_QB) . "\n\n";
+
+ my $deltaL = $per_id_QLA - $per_id_QLB;
+ my $deltaR = $per_id_QRA - $per_id_QRB;
+
+ print "DeltaL: " . sprintf("%.2f", $deltaL) . " DeltaR: " . sprintf("%.2f", $deltaR) . "\n\n";
+
+ unless ($printAlignmentsFlag) { return; }
+
+
+ ## build the left windows:
+ my @Q_left_win = @Q_chars[$win_left_end5..$win_left_end3];
+ my @A_left_win = @A_chars[$win_left_end5..$win_left_end3];
+ my @B_left_win = @B_chars[$win_left_end5..$win_left_end3];
+
+ &print_alignment($A_acc, \@A_left_win,
+ $query_acc, \@Q_left_win,
+ $B_acc, \@B_left_win);
+
+ print "\t\t** Breakpoint **\n\n";
+
+ my @Q_right_win = @Q_chars[$win_right_end5..$win_right_end3];
+ my @A_right_win = @A_chars[$win_right_end5..$win_right_end3];
+ my @B_right_win = @B_chars[$win_right_end5..$win_right_end3];
+
+ &print_alignment($A_acc, \@A_right_win,
+ $query_acc, \@Q_right_win,
+ $B_acc, \@B_right_win);
+
+ return;
+}
+
+
+####
+
+ */
}
catch(exception& e) {
int numSeqs = querySeqs.size();
+ chimeraResults.resize(numSeqs);
+ chimeraFlags.resize(numSeqs, "no");
+
//break up file if needed
int linesPerProcess = numSeqs / processors ;
float percentIdentical = maligner->getPercentID();
vector<results> Results = maligner->getOutput();
- cout << querySeqs[4]->getName() << '\t' << chimeraFlag << '\t' << percentIdentical << endl;
+ //cout << querySeqs[i]->getName() << '\t' << chimeraFlag << '\t' << percentIdentical << endl;
for (int j = 0; j < Results.size(); j++) {
- cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl;
-
+ //cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl;
}
if (chimeraFlag == "yes") {
seqs.pop_back();
}
}
-
+
//put seqs into vector to send to slayer
vector<Sequence*> seqsForSlayer;
for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
}
//send to slayer
- slayer->getResults(querySeqs[i], seqsForSlayer);
-
+ chimeraFlags[i] = slayer->getResults(querySeqs[i], seqsForSlayer);
+ chimeraResults[i] = slayer->getOutput();
+
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
vector<linePair*> lines;
vector<Sequence*> querySeqs;
vector<Sequence*> templateSeqs;
+
+ vector< vector<data_struct> > chimeraResults;
+ vector<string> chimeraFlags;
string fastafile, templateFile;
//find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
refSeqs = decalc->findClosest(query, db, numWanted);
- ofstream out;
- string outFile = "parentsOf" + query->getName();
- openOutputFile(outFile, out);
- for (int i = 0; i < refSeqs.size(); i++) { refSeqs[i]->printSequence(out); }
- out.close();
-
refSeqs = minCoverageFilter(refSeqs);
if (refSeqs.size() < 2) {
map<string, string> namesInList;
//go through listfile and get names
- for (int i = 0; i < SharedList->getNumSeqs(); i++) {
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
string names = SharedList->get(i);
-
+
while (names.find_first_of(',') != -1) {
string name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
Slayer::Slayer(int win, int increment, int parentThreshold, float div) :
windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div) {}
/***********************************************************************/
-void Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
+string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
try {
+cout << "refSeqs = " << refSeqs.size() << endl;
+ vector<data_struct> all; all.clear();
for (int i = 0; i < refSeqs.size(); i++) {
vector<data_struct> divs = runBellerophon(q, leftParent, rightParent);
+ vector<data_struct> selectedDivs;
+ for (int k = 0; k < divs.size(); k++) {
+
+ vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
+ vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
+
+ int numSNPSLeft = snpsLeft.size();
+ int numSNPSRight = snpsRight.size();
+
+ //require at least 3 SNPs on each side of the break
+ if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
+
+ int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;
+ int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1;
+
+ float snpRateLeft = numSNPSLeft / (float) winSizeLeft;
+ float snpRateRight = numSNPSRight / (float) winSizeRight;
+
+ float logR = log(snpRateLeft / snpRateRight) / log(2);
+
+ // do not accept excess snp ratio on either side of the break
+ if (abs(logR) < 1 ) {
+
+ float BS_A, BS_B;
+ bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
+
+ divs[k].bsa = BS_A;
+ divs[k].bsb = BS_B;
+
+ divs[k].bsMax = max(BS_A, BS_B);
+
+ divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+
+ selectedDivs.push_back(divs[k]);
+ }
+ }
+ }
+
+ //save selected
+ for (int m = 0; m < selectedDivs.size(); m++) { all.push_back(selectedDivs[m]); }
+
delete q;
delete leftParent;
delete rightParent;
}
-
}
+ // compute bootstrap support
+ if (all.size() > 0) {
+ //sort them
+ sort(all.begin(), all.end(), compareDataStruct);
+ reverse(all.begin(), all.end());
+
+ outputResults = all;
+ return "yes";
+ }
+ else {
+ outputResults = all;
+ return "no";
+ }
}
catch(exception& e) {
errorOut(e, "Slayer", "getResults");
}
}
/***********************************************************************/
-vector<data_struct> Slayer::runBellerophon(Sequence* query, Sequence* parentA, Sequence* parentB) {
+vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB) {
try{
vector<data_struct> data;
-
+cout << q->getName() << '\t' << q->getAligned().length() << endl;
//vertical filter
vector<Sequence*> temp;
+ temp.push_back(q); temp.push_back(pA); temp.push_back(pB);
verticalFilter(temp);
- int alignLength = query->getAligned().length();
+ //get these to avoid numerous function calls
+ string query = q->getAligned();
+ string parentA = pA->getAligned();
+ string parentB = pB->getAligned();
+ int length = query.length();
+cout << q->getName() << '\t' << length << endl;
+
+ //check window size
+ if (length < (2*windowSize+windowStep)) {
+ mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); mothurOutEndLine();
+ windowSize = length / 4;
+ }
+
+ for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
+
+ int breakpoint = i;
+ int leftLength = breakpoint + 1;
+ int rightLength = length - leftLength;
+
+ float QLA = computePercentID(query, parentA, 0, breakpoint);
+ float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
+
+ float QLB = computePercentID(query, parentB, 0, breakpoint);
+ float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
+ float LAB = computePercentID(parentA, parentB, 0, breakpoint);
+ float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
+ float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
+ float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
+ float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
+ float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
+ float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
+
+ //in original and not used
+ //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
+
+ float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
+
+ float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
+
+ //is one of them above the
+ if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
+
+ if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold)) ||
+ ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold))) {
+
+ data_struct member;
+
+ member.divr_qla_qrb = divR_QLA_QRB;
+ member.divr_qlb_qra = divR_QLB_QRA;
+ member.qla_qrb = QLA_QRB;
+ member.qlb_qra = QLB_QRA;
+ member.qla = QLA;
+ member.qrb = QRB;
+ member.ab = AB;
+ member.qa = QA;
+ member.qb = QB;
+ member.lab = LAB;
+ member.rab = RAB;
+ member.qra = QRA;
+ member.qlb = QLB;
+ member.winLStart = 0;
+ member.winLEnd = breakpoint;
+ member.winRStart = breakpoint+1;
+ member.winREnd = length-1;
+ member.querySeq = *(q);
+ member.parentA = *(pA);
+ member.parentB = *(pB);
+ member.bsa = 0;
+ member.bsb = 0;
+ member.bsMax = 0;
+ member.chimeraMax = 0;
+
+ data.push_back(member);
+
+ }//if
+ }//if
+ }//for
return data;
}
}
/***********************************************************************/
+vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
+ try {
+
+ vector<snps> data;
+
+ for (int i = left; i <= right; i++) {
+
+ char A = parentA[i];
+ char Q = query[i];
+ char B = parentB[i];
+
+ if ((A != Q) || (B != Q)) {
+ snps member;
+ member.queryChar = Q;
+ member.parentAChar = A;
+ member.parentBChar = B;
+
+ data.push_back(member);
+ }
+ }
+
+ return data;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Slayer", "getSNPS");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
+ try {
+
+ srand((unsigned)time( NULL ));
+
+ int count_A = 0; // sceneario QLA,QRB supported
+ int count_B = 0; // sceneario QLB,QRA supported
+
+ int numLeft = max(1, int(left.size()/10 +0.5));
+ int numRight = max(1, int(right.size()/10 + 0.5));
+
+ for (int i = 0; i < 100; i++) {
+ //random sampling with replacement.
+
+ vector<snps> selectedLeft;
+ for (int j = 0; j < numLeft; j++) {
+ int index = int(rand() % left.size());
+ selectedLeft.push_back(left[index]);
+ }
+
+ vector<snps> selectedRight;
+ for (int j = 0; j < numRight; j++) {
+ int index = int(rand() % right.size());
+ selectedRight.push_back(right[index]);
+ }
+
+ /* A ------------------------------------------
+ # QLA QRA
+ # Q ------------------------------------------
+ # |
+ # |
+ # Q ------------------------------------------
+ # QLB QRB
+ # B ------------------------------------------ */
+
+
+ float QLA = snpQA(selectedLeft);
+ float QRA = snpQA(selectedRight);
+
+ float QLB = snpQB(selectedLeft);
+ float QRB = snpQB(selectedRight);
+
+ //in original - not used - not sure why?
+ //float ALB = snpAB(selectedLeft);
+ //float ARB = snpAB(selectedRight);
+
+ if ((QLA > QLB) && (QRB > QRA)) {
+ count_A++;
+ }
+
+ if ((QLB > QLA) && (QRA > QRB)) {
+ count_B++;
+ }
+
+ }
+
+ BSA = (float) count_A;
+ BSB = (float) count_B;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Slayer", "bootstrapSNPS");
+ exit(1);
+ }
+}
+/***********************************************************************/
+float Slayer::snpQA(vector<snps> data) {
+ try {
+
+ int numIdentical = 0;
+
+ for (int i = 0; i < data.size(); i++) {
+ if (data[i].parentAChar == data[i].queryChar) {
+ numIdentical++;
+ }
+ }
+
+ float percentID = (numIdentical / data.size()) * 100;
+
+ return percentID;
+ }
+ catch(exception& e) {
+ errorOut(e, "Slayer", "snpQA");
+ exit(1);
+ }
+}
+/***********************************************************************/
+float Slayer::snpQB(vector<snps> data) {
+ try {
+
+ int numIdentical = 0;
+
+ for (int i = 0; i < data.size(); i++) {
+ if (data[i].parentBChar == data[i].queryChar) {
+ numIdentical++;
+ }
+ }
+
+ float percentID = (numIdentical / data.size()) * 100;
+
+ return percentID;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Slayer", "snpQB");
+ exit(1);
+ }
+}
+/***********************************************************************/
+float Slayer::snpAB(vector<snps> data) {
+ try {
+ int numIdentical = 0;
+
+ for (int i = 0; i < data.size(); i++) {
+ if (data[i].parentAChar == data[i].parentBChar) {
+ numIdentical++;
+ }
+ }
+
+ float percentID = (numIdentical / data.size()) * 100;
+
+ return percentID;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Slayer", "snpAB");
+ exit(1);
+ }
+}
+/***********************************************************************/
float Slayer::computePercentID(string queryFrag, string parent, int left, int right) {
try {
int total = 0;
}
}
/***********************************************************************/
-//this is a vertical filter
+//remove columns that contain any gaps
void Slayer::verticalFilter(vector<Sequence*> seqs) {
try {
vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
- if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
+ if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; }
}
}
//zero out spot where all sequences have blanks
int numColRemoved = 0;
+
for(int i = 0; i < seqs[0]->getAligned().length(); i++){
- if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
+ if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; }
}
-
+
//for each sequence
for (int i = 0; i < seqs.size(); i++) {
/***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
-struct data_struct { //not right needs work...
- int regionStart;
- int regionEnd;
- string parent;
- float queryToParent;
- float queryToParentLocal;
- float divR;
+struct data_struct { //this is crazy big...but follow original.
+ float divr_qla_qrb;
+ float divr_qlb_qra;
+ float qla_qrb;
+ float qlb_qra;
+ float qla;
+ float qrb;
+ float ab;
+ float qa;
+ float qb;
+ float lab;
+ float rab;
+ float qra;
+ float qlb;
+ int winLStart;
+ int winLEnd;
+ int winRStart;
+ int winREnd;
+ Sequence querySeq;
+ Sequence parentA;
+ Sequence parentB;
+ float bsa;
+ float bsb;
+ float bsMax;
+ float chimeraMax;
+
};
/***********************************************************************/
+//sorts lowest to highest first by bsMax, then if tie by chimeraMax
+inline bool compareDataStruct(data_struct left, data_struct right){
+ if (left.bsMax < right.bsMax) { return true; }
+ else if (left.bsMax == right.bsMax) {
+ return (left.chimeraMax < right.chimeraMax);
+ }else { return false; }
+}
+/***********************************************************************/
+struct snps {
+ char queryChar;
+ char parentAChar;
+ char parentBChar;
+};
+
+/***********************************************************************/
class Slayer {
Slayer(int, int, int, float);
~Slayer() {};
- void getResults(Sequence*, vector<Sequence*>);
- //float getPercentID() { return percentIdenticalQueryChimera; }
- //vector<results> getOutput() { return outputResults; }
+ string getResults(Sequence*, vector<Sequence*>);
+ vector<data_struct> getOutput() { return outputResults; }
private:
int windowSize, windowStep, parentFragmentThreshold;
float divRThreshold;
+ vector<data_struct> outputResults;
void verticalFilter(vector<Sequence*>);
float computePercentID(string, string, int, int);
vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
-
+ vector<snps> getSNPS(string, string, string, int, int);
+ void bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+ float snpQA(vector<snps>);
+ float snpQB(vector<snps>);
+ float snpAB(vector<snps>);
};
projects / mothur.git / commitdiff