Rename Fcr and FcrData classes to FcrWriter and FcrReader, respectively

Author: iainrb

Fcr.cpp

@@ -50,11 +50,11 @@ using namespace std;
 
 const static double pi = 3.141593;
 
-Fcr::Fcr() {
+FcrWriter::FcrWriter() {
   // empty constructor
 }
 
-double Fcr::BAF(double theta, Egt egt, long snpIndex) {
+double FcrWriter::BAF(double theta, Egt egt, long snpIndex) {
   // estimate the B allele frequency by interpolating between known clusters
   float *meanTheta = new float[egt.GENOTYPES_PER_SNP];
   egt.getMeanTheta(snpIndex, meanTheta);
@@ -73,7 +73,7 @@ double Fcr::BAF(double theta, Egt egt, long snpIndex) {
 }
 
 // sanity check on manifest and gtc file
-void Fcr::compareNumberOfSNPs(Manifest *manifest, Gtc *gtc) {
+void FcrWriter::compareNumberOfSNPs(Manifest *manifest, Gtc *gtc) {
   if (manifest->snps.size() != gtc->xRawIntensity.size()) {
     ostringstream msg;
     msg << "Size mismatch: Manifest contains " << manifest->snps.size() 
@@ -84,7 +84,7 @@ void Fcr::compareNumberOfSNPs(Manifest *manifest, Gtc *gtc) {
   }
 }
 
-void Fcr::illuminaCoordinates(double x, double y, double &theta, double &r) {
+void FcrWriter::illuminaCoordinates(double x, double y, double &theta, double &r) {
   // convert (x,y) cartesian coordinates to Illumina coordinates (theta, r)
   // these are ***NOT*** standard polar coordinates!
   // the angle theta is rescaled s.t. pi/2 radians = 1 "Illumina angular unit"
@@ -94,7 +94,7 @@ void Fcr::illuminaCoordinates(double x, double y, double &theta, double &r) {
 
 }
 
-string Fcr::createHeader(string content, int samples, int snps) {
+string FcrWriter::createHeader(string content, int samples, int snps) {
   // generate standard FCR header
   // content argument is typically the manifest name
   // includes data set summary, and column heads for main body
@@ -127,7 +127,7 @@ string Fcr::createHeader(string content, int samples, int snps) {
   return header;
 }
 
-double Fcr::logR(double theta, double r, Egt egt, long snpIndex) {
+double FcrWriter::logR(double theta, double r, Egt egt, long snpIndex) {
   // calculate the LogR metric for given (theta, r) of sample
   // snpIndex is position in the manifest (starting from 0)
   // get (theta, R) for AA, AB, BB from EGT and interpolate
@@ -151,7 +151,7 @@ double Fcr::logR(double theta, double r, Egt egt, long snpIndex) {
 }
 
 
-void Fcr::write(Egt *egt, Manifest *manifest, ostream *outStream, 
+void FcrWriter::write(Egt *egt, Manifest *manifest, ostream *outStream, 
               vector<string> infiles, vector<string> sampleNames) {
   // 'main' method to generate FCR and write to given output stream
  Gtc *gtc = new Gtc();
@@ -207,7 +207,7 @@ void Fcr::write(Egt *egt, Manifest *manifest, ostream *outStream,
 } 
 
 
-FcrData::FcrData(string infile) {
+FcrReader::FcrReader(string infile) {
   ifstream inStream;
   string line;
   bool body = false;
@@ -268,8 +268,8 @@ FcrData::FcrData(string infile) {
   this->header = parseHeader(header_lines);
 }
 
-bool FcrData::equivalent(FcrData other, bool verbose) {
-  // check for equality on data fields with another FcrData object
+bool FcrReader::equivalent(FcrReader other, bool verbose) {
+  // check for equality on data fields with another FcrReader object
   bool equal = true;
   double epsilon = 1e-5;
   if (totalPairs != other.totalPairs) {
@@ -370,7 +370,7 @@ bool FcrData::equivalent(FcrData other, bool verbose) {
 
 }
 
-bool FcrData::equivalentHeaders(FcrData other, bool verbose) {
+bool FcrReader::equivalentHeaders(FcrReader other, bool verbose) {
   map<string, string> myHead = this->header;
   map<string, string> otherHead = other.header;
   bool equivalent = true;
@@ -392,7 +392,7 @@ bool FcrData::equivalentHeaders(FcrData other, bool verbose) {
   return equivalent;
 }
 
-map<string, string> FcrData::parseHeader(vector<string> input) {
+map<string, string> FcrReader::parseHeader(vector<string> input) {
   // parse header fields
   vector<unsigned int> keyLengths(headerKeys.size(), 0);
   for (unsigned int i=0; i<headerKeys.size(); i++) {
@@ -422,7 +422,7 @@ map<string, string> FcrData::parseHeader(vector<string> input) {
   return header;
 }
 
-vector<string> FcrData::splitByWhiteSpace(string str) {
+vector<string> FcrReader::splitByWhiteSpace(string str) {
   // split line into tokens by iterating over a stringstream
   string buffer; 
   stringstream ss(str); // Insert the string into a stream

Fcr.h

@@ -42,10 +42,10 @@
 
 using namespace std;
 
-class Fcr {
+class FcrWriter {
 
  public:
-  Fcr();
+  FcrWriter();
   double BAF(double theta, Egt egt, long snpIndex);
   void compareNumberOfSNPs(Manifest *manifest, Gtc *gtc);
   void illuminaCoordinates(double x, double y, double &theta, double &r);
@@ -55,7 +55,7 @@ class Fcr {
 
 };
 
-class FcrData {
+class FcrReader {
  // Container for data in an FCR file
  // Intended only for running tests
  // "Real" FCR files are typically too big to slurp into memory
@@ -65,7 +65,7 @@ class FcrData {
   string fileKey;
   vector<string> headerKeys;
   map<string, string> header;
-  FcrData(string infile);
+  FcrReader(string infile);
   vector<string> snps;
   vector<string> samples;
   vector<string> alleles_a;
@@ -79,10 +79,10 @@ class FcrData {
   vector<int> y_raw;
   vector<double> logR;
   vector<double> baf;
-  bool equivalent(FcrData other, bool verbose=true);
+  bool equivalent(FcrReader other, bool verbose=true);
 
  private:
-  bool equivalentHeaders(FcrData other, bool verbose=true);
+  bool equivalentHeaders(FcrReader other, bool verbose=true);
   map<string, string> parseHeader(vector<string> header);
   vector<string> splitByWhiteSpace(string str);
 

commands.cpp

@@ -257,7 +257,7 @@ void Commander::commandFCR(string infile, string outfile, string manfile, string
   vector<string> infiles;	// list of GTC files to process
   Manifest *manifest = new Manifest();
   Egt *egt = new Egt();
-  Fcr *fcr = new Fcr(); // Final Call Report generator
+  FcrWriter *fcrWriter = new FcrWriter(); // Final Call Report generator
   ofstream outFStream;
   ostream *outStream;
   if (outfile == "-") {
@@ -272,9 +272,10 @@ void Commander::commandFCR(string infile, string outfile, string manfile, string
   egt->open(egtfile);
   // now we have output stream, GTC paths, populated manifest and EGT
   // write output to an FCR file
-  fcr->write(egt, manifest, outStream, infiles, sampleNames);
+  fcrWriter->write(egt, manifest, outStream, infiles, sampleNames);
   delete manifest;
   delete egt;
+  delete fcrWriter;
 }
 
 

test_simtools.h

@@ -207,28 +207,28 @@ class FcrTest : public TestBase
 {
  public:
 
-  void testFcrClass(void)
+  void testFcrWriterClass(void)
   {
     string infile = "data/humancoreexome-12v1-1_a.egt";
-    Fcr *fcr;
+    FcrWriter *fcrWriter;
     Egt *egt;
     egt = new Egt();
     egt->open(infile);
-    TS_ASSERT_THROWS_NOTHING(new Fcr());
-    fcr = new Fcr();
+    TS_ASSERT_THROWS_NOTHING(new FcrWriter());
+    fcrWriter = new FcrWriter();
     double r;
     double theta;
     double x = 3.0;
     double y = 4.0;
-    fcr->illuminaCoordinates(x, y, theta, r);
+    fcrWriter->illuminaCoordinates(x, y, theta, r);
     TS_ASSERT_DELTA(r, 7.0, 1e-6);
     TS_ASSERT_DELTA(theta, 0.5903345, 1e-6);
-    double baf = fcr->BAF(0.738881, *egt, 0);
+    double baf = fcrWriter->BAF(0.738881, *egt, 0);
     TS_ASSERT_DELTA(baf, 0.75, 1e-6);
-    double logR = fcr->logR(1, 0.73881, *egt, 0);
+    double logR = fcrWriter->logR(1, 0.73881, *egt, 0);
     TS_ASSERT_DELTA(logR, -0.7180, 1e-4);
     delete egt;
-    delete fcr;
+    delete fcrWriter;
   }
 };
 
@@ -331,14 +331,14 @@ class SimtoolsTest : public TestBase
     int size = 4657; // expected file size
     assertFileSize(outfile, size);
     TS_TRACE("FCR output file is of expected length");
-    FcrData data_ref = FcrData(normfile);
+    FcrReader data_ref = FcrReader(normfile);
     TS_ASSERT(data_ref.totalPairs == 50);
     TS_ASSERT(data_ref.snps.size() == 50);
     TS_ASSERT(data_ref.samples.size() == 50);
     TS_ASSERT(data_ref.header["Num SNPs"].compare("10")==0);
     TS_ASSERT(data_ref.header["Num Samples"].compare("5")==0);
     TS_ASSERT(data_ref.equivalent(data_ref));
-    FcrData data_test = FcrData(outfile);
+    FcrReader data_test = FcrReader(outfile);
     TS_TRACE("Created and tested FCRData objects"); 
     TS_ASSERT(data_ref.equivalent(data_test));
     TS_TRACE("FCR output file is equivalent to reference copy");