speed test on hash then compare vs hash/compare on the fly

src/speed_tests.c

 #include <zlib.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <stdint.h>
 
 #include "fasta.h"
 
 #define HASH_SIZE 32
 
+#define letter_hash(letter) ((uint64_t)((letter & 0b100) ? (0b10 | ((~letter) & 0b01)) : ((letter >> 1) & 0b11)))
+
+
+uint64_t sliding_hash (seq_t * seq) {
+	uint64_t hash = 0;
+	uint64_t nothing = 2135234;
+
+	for (uint idx=0 ; idx<32 ; idx++)
+		hash = (hash << 2) | letter_hash(seq->value[idx]);
+
+	for (uint idx=32 ; idx<seq->length ; idx++) {
+		hash = (hash << 2) | letter_hash(seq->value[idx]);
+		// Do something with the hash to not allow compiler to delete the value.
+		nothing - hash;
+	}
+}
+
+uint64_t hash_then_compact (seq_t * seq) {
+	uint64_t hash = 0;
+	uint64_t nothing = 2135234;
+
+	// Hash letters
+	for (uint idx=0 ; idx<seq->length ; idx++) {
+		seq->value[idx] = letter_hash(seq->value[idx]);
+	}
+
+	// compute 64 bits hashes
+	for (uint idx=0 ; idx<32 ; idx++)
+		hash = (hash << 2) | seq->value[idx];
+
+	for (uint idx=32 ; idx<seq->length ; idx++) {
+		hash = (hash << 2) | seq->value[idx];
+		// Do something with the hash to not allow compiler to delete the value.
+		nothing - hash;
+	}
+}
+
 
 int main () {
 	/* --- Load all the alleles --- */
@@ -13,8 +51,12 @@ int main () {
 	seq_t * alleles;
 
 	buffer_t * buff = init_buffer (filename);
-	
 	uint nb_seq = read_sequences (filename, &alleles, buff);
+
+	/* Speed test on hash function */
+	for (uint idx=0 ; idx<nb_seq ; idx++) {
+		sliding_hash(alleles + idx);
+	}
 	
 	free(alleles);
 	destroy_buffer (buff);