Thomas Hume's C code. See http://saml.rilspace.org/node/248

gc_ThomasHume.c

#include <stdio.h>
#include <assert.h>

int main() {
    FILE * inputFile = fopen( "Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa", "rb" );

    size_t gcCount = 0;
    size_t atCount = 0;

    for ( char c; (c = fgetc_unlocked( inputFile )) != EOF; ) {
        if ( c == '>' ) {
            while ( (c = fgetc_unlocked( inputFile )) != '\n' )
                ;
        } else {
            do {
                switch ( c ) {
                	case 'A':
                	case 'T':
                    	atCount++;
                    break;

                	case 'G':
                	case 'C':
                    	gcCount++;
                    break;

                	default:
                    break;
                }
            } while ( (c = fgetc_unlocked( inputFile )) != '\n' );
        }
    }
    int totalBaseCount = atCount + gcCount;
    printf( "%f\n", ((float)gcCount / (float)totalBaseCount ) * 100 );
    return 0;
}

Compile flags used:

gcc -ogc_c_th -std=gnu99 -O3 gc_th.c