Example Documentation

/*
  $Id: libSliceExample.c,v 1.1 2005/07/29 02:55:17 mschatz Exp $
  
  Simple Example of how to use the C interface to libSlice
*/

#include <stdio.h>
#include <stdlib.h>
#include "Slice.h"

int main(int argc, char ** argv)
{
  int dcov = 4;
  int len  = 3;
  int i;

  libSlice_Slice *s = libSlice_newmem(len, sizeof(libSlice_Slice));

  for (i = 0; i < len; i++)
  {
    s[i].bc = libSlice_newmem(dcov, sizeof(char));
    s[i].qv = libSlice_newmem(dcov, sizeof(char));
    s[i].rc = libSlice_newmem(dcov, sizeof(char));
    s[i].dcov = dcov;
  }

  s[0].c = 'A';
  s[0].bc[0] = 'A'; s[0].bc[1] = 'A'; s[0].bc[2] = 'T'; s[0].bc[3] = 'C';
  s[0].qv[0] = 30;  s[0].qv[1] = 25;  s[0].qv[2] = 20;  s[0].qv[3] = 15; 
  s[0].rc[0] = 1;   s[0].rc[1] = 1;   s[0].rc[2] = 0;   s[0].rc[3] = 0;
  
  s[1].c = 'T';
  s[1].bc[0] = 'T'; s[1].bc[1] = 'T'; s[1].bc[2] = 'T'; s[1].bc[3] = 'T';
  s[1].qv[0] = 30;  s[1].qv[1] = 30;  s[1].qv[2] = 20;  s[1].qv[3] = 15;
  s[1].rc[0] = 1;   s[1].rc[1] = 0;   s[1].rc[2] = 1;   s[1].rc[3] = 0;

  s[2].c = 'Y';
  s[2].bc[0] = 'C'; s[2].bc[1] = 'T'; s[2].bc[2] = 'C'; s[2].bc[3] = 'T';
  s[2].qv[0] = 30;  s[2].qv[1] = 30;  s[2].qv[2] = 30;  s[2].qv[3] = 30;
  s[2].rc[0] = 1;   s[2].rc[1] = 1;   s[2].rc[2] = 0;   s[2].rc[3] = 0;

  for (i = 0; i < len; i++)
  {
    int j;
    printf("\nslice i=%d, c=%c, dcov=%d\n", i, s[i].c, s[i].dcov);

    for (j = 0; j < s[i].dcov; j++)
    {
      printf("  j=%d bc=%c qv=%d rc=%d\n", j, s[i].bc[j], s[i].qv[j], s[i].rc[j]);
    }
  }

  // ================================= //
  //   testing getConsQC(),getCons()   //
  // ================================= //
  {
    libSlice_Consensus result;
    libSlice_getConsensus(&s[0], &result, NULL, 0);

    printf("\ntesting getConsQC(), getConsensus()\n");
    printf("slice i=0 c=%c qc=%d qv=%d\n", 
           result.consensus,
           libSlice_getConsQC(&s[0], 0), 
           result.qvConsensus);

    printf("[qvA=%d qvC=%d qvG=%d qvT=%d qvGap=%d]\n\n", 
           result.qvA, 
           result.qvC, 
           result.qvG, 
           result.qvT, 
           result.qvGap);
  }

  // =========================================== //
  //   testing getConsQCRange(),getConsRange()   //
  // =========================================== //
  {
    libSlice_Consensus results [len];

    char *qc = libSlice_getConsQCRange(s, len, 0);
    libSlice_getConsensusRangeWithAmbiguity(s, results, len, NULL, 0);

    printf("testing getConsQCRange(), getConsensusRange()\n");
    for (i = 0; i < len; i++)
    {
      printf("slice i=%d c=%c qc=%d qv=%d\n", 
             i,
             results[i].consensus,
             qc[i], 
             results[i].qvConsensus);

      printf("[qvA=%d qvC=%d qvG=%d qvT=%d qvGap=%d]\n\n", 
             results[i].qvA, 
             results[i].qvC, 
             results[i].qvG, 
             results[i].qvT, 
             results[i].qvGap);
    }

    free(qc);
  }

  for (i = 0; i < len; i++)
  {
    free(s[i].bc);
    free(s[i].qv);
    free(s[i].rc);
  }

  free(s);
  return 0;
}