Example Documentation

#include <list>
#include <SliceData.hh>


int main (int argc, char ** argv)
{
  libSlice::ReadManager r;

  r.addReadData("DMGLN85TF", "", "Forward", "");
  r.addReadData("DMGHB30TR", "", "Reversed", "");
  r.addReadData("DMGIC39TF", "", "Forward", "");
  r.addReadData("DMGRA39TR", "", "Reversed", "");

  libSlice::SliceData s1(r, "Location 1", "", "");
  libSlice::SliceData s2(r, "Location 2", "", "");
  libSlice::SliceData s3(r, "Location 3", "", "");

  s1.addNuc("AATC");
  s1.addReadId("DMGHB30TR DMGRA39TR DMGLN85TF DMGIC39TF");
  s1.addQualVal("30 25 20 15");

  s2.addNuc("TTTT");
  s2.addReadId("DMGHB30TR DMGLN85TF DMGRA39TR DMGIC39TF");
  s2.addQualVal("30 30 20 15");

  s3.addNuc("CTCT");
  s3.addReadId("DMGHB30TR DMGRA39TR DMGLN85TF DMGIC39TF");
  s3.addQualVal("30 30 30 30");

  list<libSlice::SliceData> slicelist;

  slicelist.push_back(s1);
  slicelist.push_back(s2);
  slicelist.push_back(s3);

  try
  {
    list<libSlice::SliceData>::iterator i;

    for (i = slicelist.begin(); i != slicelist.end(); i++)
    {

      i->print(cout);

      libSlice::ConsensusData result = i->doCalculations();
      cout << endl
           << "Consensus is "     << result.getConsensus()     << endl
           << "Quality Base is "  << result.getConsensusBase() << endl
           << "Quality Class is " << result.getQualityClass()  << endl
           << "Quality Value is " << result.getQualityValue()  << endl;

      cout << "[qvA="   << result.getQualityValue('A')
           <<  " qvC="   << result.getQualityValue('C')
           <<  " qvG="   << result.getQualityValue('G')
           <<  " qvT="   << result.getQualityValue('T')
           <<  " qvGap=" << result.getQualityValue('-')
           <<  "]" << endl;

      cout << endl;
    }
  }
  catch (const Exception & e)
  {
    cerr << e << endl;
    return 10;
  }

  return 0;
}
SliceDataExample.cc
