// Iterates through a string and maps all the nucleotides to their enum counter
// Returns length of white-space elimited mapped string, now in buffer, which was
// updated by reference.
size_t clear_whitespaces_do_mapping ( signed char* buffer, long size ) {
size_t non_ws_index = 0, traverse_index = 0;
while ( traverse_index < size ) {
char curr_char = buffer[traverse_index];
switch ( curr_char ) {
case 'A': case 'C': case 'G': case 'T':
/*this used to be a copy not also does mapping*/
buffer[non_ws_index++] = char_mapping(curr_char);
break;
}
++traverse_index;
}
return non_ws_index;
}
static size_t read_sequence(FILE *file, int fnum, signed char *dest, size_t fsize) {
fread(dest, sizeof(char), fsize, file);
size_t seqlen = 0, traverse_index = 0;
while ( traverse_index < fsize ) {
char curr_char = dest[traverse_index];
switch ( curr_char ) {
case 'A': case 'C': case 'G': case 'T':
dest[seqlen++] = char_mapping(curr_char);
break;
}
++traverse_index;
}
dest[seqlen] = '\0';
PRINTF("Size of input sequence %d has length %zu\n", fnum, seqlen);
return seqlen;
}
