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/*
* ref_aligner.cpp
*/
/**
* Maps an octet representing the XOR of two two-bit-per-base-encoded
* DNA sequences to the number of bases that mismatch between the two.
*
* Generated with this perl:
*
* print "const unsigned char u8toMms[] = {\n";
* for(my $i = 0; $i < 256; $i++) {
* if(($i & 7) == 0) {
* print "\t";
* }
* my $c = $i;
* my $mms = 0;
* for(my $j = 0; $j < 4; $j++) {
* if(($c & 3) != 0) {
* $mms++;
* }
* $c >>= 2;
* }
* print "$mms, ";
* if(($i & 7) == 7) {
* print "\n";
* }
* }
* print "};\n";
*
*/
unsigned char u8toMms[] = {
0, 1, 1, 1, 1, 2, 2, 2,
1, 2, 2, 2, 1, 2, 2, 2,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
1, 2, 2, 2, 2, 3, 3, 3,
2, 3, 3, 3, 2, 3, 3, 3,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
2, 3, 3, 3, 3, 4, 4, 4,
3, 4, 4, 4, 3, 4, 4, 4,
};
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