ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c

   1 #include <stdint.h>     /* We save the all the frequencies in a 64 bit int */
   2 #include <stdio.h>      /* We extract/add them using bitshifts */
   3 #include <stdlib.h>     /* When no filepath is specified assume stdin */
   4 #include <string.h>
   5
   6 int main(int argc, char* argv[])
   7 {
   8         char *alphabet = "AGTC";
   9         char c;
  10         int charsperline = 0;
  11         int numlines = 0;
  12         uint64_t occs = 0;
  13         FILE *f = argc != 2 ? stdin : fopen(argv[1], "r");
  14         if(f == NULL)
  15                 return 2;
  16         while((c = fgetc(f)) != EOF)
  17                 if(c == '\n' && charsperline == 100 && numlines++ < 500)
  18                         charsperline = 0;
  19                 else if(strchr(alphabet, c) && charsperline++ < 100)
  20                         occs += 1LL<<((int)(strchr(alphabet, c)-alphabet)*16);
  21                 else
  22                         break;
  23         if(f != stdin)
  24                 fclose(f);
  25         if(numlines != 500)
  26                 return -1;
  27         for(unsigned i=0; i<strlen(alphabet); i++)
  28                 printf("%c: %u\n", alphabet[i], (uint16_t)(occs >> (16*i)));
  29         return 0;
  30 }