--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gecko/src/dictionaryFunctions.c	Thu Dec 13 07:59:25 2018 -0500
@@ -0,0 +1,94 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <inttypes.h>
+#include "structs.h"
+#include "commonFunctions.h"
+
+int seq2word(char* buf, int wsize, word* w) {
+	int i;
+	int b = 6;
+	memset(w, 0, sizeof(word));
+
+	for (i = 0; i < wsize; i++) {
+		if (buf[i] >= 4)
+			return -1;
+		w->b[i / 4] |= buf[i] << b;
+		b -= 2;
+		if (b < 0)
+			b = 6;
+	}
+	return 0;
+}
+
+void skipIDLine(FILE *fIn) {
+	char c;
+	// first line (skip ID fasta Line)
+	c = fgetc(fIn);
+	while (c != '\n')
+		c = fgetc(fIn);
+}
+
+int letterToIndex(char c) {
+	// coding (a=0,c=1,g=2,t=3,'>'=4 others=9 )
+	switch (c) {
+	case 'A':
+		return 0;
+	case 'C':
+		return 1;
+	case 'G':
+		return 2;
+	case 'T':
+		return 3;
+	case '>':
+		return 4;
+	default:
+		return 9;
+	}
+}
+
+int wordcmp(unsigned char *w1, unsigned char *w2, int n) {
+
+	int i = 0, limit;
+
+	if(n%4 != 0){
+		w1[n/4] = w1[n/4] >> (2*(3-((n-1)%4)));
+		w1[n/4] = w1[n/4] << (2*(3-((n-1)%4)));
+		w2[n/4] = w2[n/4] >> (2*(3-((n-1)%4)));
+		w2[n/4] = w2[n/4] << (2*(3-((n-1)%4)));
+		limit=(n/4)+1;
+	} else {
+		limit = n/4;
+	}
+
+	for (i=0;i<limit;i++) {
+		if (w1[i]<w2[i]) return -1;
+		if (w1[i]>w2[i]) return +1;
+	}
+	return 0;
+}
+
+void showWord(word* w, char *ws) {
+	char Alf[] = { 'A', 'C', 'G', 'T' };
+	int i;
+	int wsize = 8;
+	unsigned char c;
+	for (i = 0; i < wsize; i++) {
+		c = w->b[i];
+		c = c >> 6;
+		ws[4*i] = Alf[(int) c];
+		c = w->b[i];
+		c = c << 2;
+		c = c >> 6;
+		ws[4*i+1] = Alf[(int) c];
+		c = w->b[i];
+		c = c << 4;
+		c = c >> 6;
+		ws[4*i+2] = Alf[(int) c];
+		c = w->b[i];
+		c = c << 6;
+		c = c >> 6;
+		ws[4*i+3] = Alf[(int) c];
+	}
+}