--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMSAME/src/combine_reads.c	Sat Dec 15 18:04:10 2018 -0500
@@ -0,0 +1,128 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "structs.h"
+#include "commonFunctions.h"
+
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+#define MIN(x, y) (((x) <= (y)) ? (x) : (y))
+#define STARTING_SEQS 1000
+#define PIECE_OF_DB_REALLOC 3200000 //half a gigabyte if divided by 8 bytes
+#define MATVAL 101
+
+// void terror(char *s) {
+//     fprintf(stdout, "ERR**** %s ****\n", s);
+//     exit(-1);
+// }
+
+
+int main(int argc, char ** av){
+    
+    if(argc != 2) terror("USE:: combine_reads <file>");
+
+	
+    char names[10][100] = {"14np", "47np", "BR0716C", "BR11044P", "CA01044C", "CA01067C", "CA11149P", "CA11154P", "MA07066C", "MA09032P"};
+    uint64_t llen[10] = {1758451, 959020, 1616163, 884193, 934256, 1007436, 1670521, 584151, 671010, 516632};
+    uint64_t nseqs = 10;
+
+    FILE * results, * data;
+    data = fopen(av[1], "rt");
+    if(data == NULL) terror("Could not open input file");
+
+    uint64_t * mat = (uint64_t *) calloc(MATVAL, sizeof(uint64_t));
+    if(mat == NULL) terror("Could not allocate matrix array");
+    long double * mat_e = (long double *) calloc(MATVAL, sizeof(long double));
+    if(mat_e == NULL) terror("Could not allocate float table");
+
+    char current_file[100];
+    uint64_t i=5, idx=0;
+    while(av[1][i] != '_' && av[1][i+1] != 'g'){
+	    current_file[idx++] = av[1][i];
+	    i++;
+    }
+    current_file[idx] = '\0';
+    fprintf(stdout, "Current file is %s\n", current_file);
+
+    char buffer[MAXLID];
+    if ((results = fopen("accu.log", "r")) == NULL){
+        results = fopen("accu.log", "wt");
+    }else{
+        // Load the matrix
+       
+        
+        for(i=0;i<100;i++){
+            if(0 == fgets(buffer, MAXLID, results)) terror("Missing number on load");
+            
+            //fprintf(stdout, "Have %s\n", buffer);
+            buffer[strlen(buffer)-1] = '\0';
+            //mat[i] = asciiToUint64(buffer);
+	    mat_e[i] = (long double) atof(buffer);
+            //fprintf(stdout, "%"PRIu64"\n", mat[i]);
+            //getchar();
+        }
+        fclose(results);
+        results = fopen("accu.log", "wt"); // Re open
+    }
+
+    // Read file 
+    uint64_t read_id_1, read_id_2, coverage, identity, length, current, currmax, j, last = 100000, lastmax = 0xFFFFFFFFFFFFFFFF;
+    while(!feof(data)){
+        if(0 == fgets(buffer, MAXLID, data) && !feof(data)) terror("Missing values");
+        // 2 77277 89 64 213
+        sscanf(buffer, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64, &read_id_1, &read_id_2, &coverage, &identity, &length);
+        //fprintf(stdout, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64"\n", read_id_1, read_id_2, coverage, identity, length);
+        currmax = MIN(identity, coverage);
+        //fprintf(stdout, "%"PRIu64"\n", currmax);
+        current = read_id_1;
+        /*
+        for(j=currmax; j > 1; j--){
+            if(current != lasts[j]){
+                mat[j]++;
+                lasts[j] = current;
+            }
+        }
+        */
+	if(lastmax == 0xFFFFFFFFFFFFFFFF){
+		last = current;
+		lastmax = 0;
+	}
+	if(current == last){
+		//mat[currmax] += 1;
+		if(lastmax < currmax){
+			lastmax = currmax;
+		}
+	}else{
+		mat[lastmax]++;
+		last = current;
+		lastmax = 0;
+	}
+
+    }
+
+    uint64_t divider = 0;
+    for(i=0; i < nseqs; i++){
+
+	    if(strcmp(current_file, names[i]) == 0){
+		    divider = llen[i];
+	    }
+    }
+    if(divider == 0) terror("Could not find file for divider"); else fprintf(stdout, "The divider is %"PRIu64"\n", divider);
+
+    for(j=99; j>0; j--){
+        mat[j] += mat[j+1];
+    }
+    mat[0] = mat[1];
+
+    for(j=0; j<100; j++){
+        fprintf(stdout, "%"PRIu64" --> %.5f\n", mat[j], (float)((100*(long double)mat[j])/(long double)divider));
+	
+        fprintf(results, "%.5f\n", (float)(mat_e[j] + ((100*(long double)mat[j])/(long double)divider))/2);
+    }
+
+
+    fclose(results);
+    fclose(data);
+    free(mat);
+    return 0;
+}