sim.cpp

// 
// sim.cpp
//
// Program to read the contents of a GTC file
//
// $Id: sim.cpp 1354 2010-11-11 16:20:09Z js10 $
//
// Copyright (c) 2009 - 2010 Genome Research Ltd.
//
// Author: Jennifer Liddle <js10@sanger.ac.uk, jennifer@jsquared.co.uk>
//
// Redistribution and use in source and binary forms, with or without 
// modification, are permitted provided that the following conditions are met:
// 1. Redistributions of source code must retain the above copyright notice, 
// this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright 
// notice, this list of conditions and the following disclaimer in the 
// documentation and/or other materials provided with the distribution.
// 3. Neither the name of Genome Research Ltd nor the names of the 
// contributors may be used to endorse or promote products derived from 
// software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR 
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
// IN NO EVENT SHALL GENOME RESEARCH LTD. BE LIABLE FOR ANY DIRECT, INDIRECT, 
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF 
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF 
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//

#include <iostream>
#include <vector>
#include <map>
#include "stdlib.h" 
#include "Sim.h"

using namespace std;

int main(int argc, char *argv[])
{
  // Simple executable to demonstrate use of the .sim class
  // Similar functionality to "simtools view"

        if (argc!=3) {
	  cout << "Usage: " << argv[0] << " [path to .sim file] " 
	       << "[max intensities to display per sample]" << endl;
	  exit(1);
	}
	Sim *sim = new Sim();
	string m;
	cout << endl << "Reading SIM file: " << argv[1] << endl;
	try { sim->openInput(argv[1]); } 
	catch (string m) { cout << m << endl; }

	int maxDisplay;
	maxDisplay = atoi(argv[2]);

	cout << "Magic:     " << sim->magic << endl;
	cout << "Version:   " << (int)sim->version << endl;
	cout << "Name Size: " << sim->sampleNameSize << endl;
	cout << "Samples:   " << sim->numSamples << endl;
	cout << "Probes:    " << sim->numProbes << endl;
	cout << "Channels:  " << (int)sim->numChannels << endl;
	cout << "Format:    " << (int)sim->numberFormat << endl;

	cout << endl;
	char *sampleName = new char[sim->sampleNameSize+1];
	
	uint16_t *intensity_int = 
	  (uint16_t *) calloc(sim->sampleIntensityTotal, sizeof(uint16_t));
	float *intensity_float = 
	  (float *) calloc(sim->sampleIntensityTotal, sizeof(float));

	unsigned int i;
	int j;
	int displayTotal = min(sim->sampleIntensityTotal, maxDisplay);
	for (i=0; i < sim->numSamples; i++) {
		if (sim->numberFormat == 0) {
		  sim->getNextRecord(sampleName, intensity_float);
		} else { 
		  sim->getNextRecord(sampleName, intensity_int);
		}
		cout << sampleName << "\t: ";
		for (j=0; j<displayTotal; j++) {
		  if (sim->numberFormat == 0) {
		    cout << intensity_float[j] << " "; 
		  } else {
		    cout << intensity_int[j] << " ";
		  }
		}
		cout << endl;
	}
	sim -> reportNonNumeric();
	free(intensity_int);
	free(intensity_float);
	sim->close();
	delete sim;
	return 0;
}