1 files changed, 87 insertions, 34 deletions

diff --git a/kmer_total_count.c b/kmer_total_count.c
index fd8a676..b0bf23f 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -1,59 +1,112 @@
 // Copyright 2013 Calvin Morrison
 #include <errno.h>
+#include <stdbool.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include <getopt.h>
 
 #include "kmer_utils.h"
 
 int main(int argc, char **argv) {
 
+
+	char *filename = NULL;
+
+	unsigned int kmer = NULL;
+
+	bool nonzero = 0;
+	bool label = 0;
+	bool kmer_set = 0;
+
+	unsigned long long width = 0;
+
   unsigned long long i = 0;
+
   long long j = 0;
 
-  if(argc <  3) {
-    fprintf(stderr, "Please supply a filename and a kmer, then as many kmers as you want (in ACGT format)\n");
-    exit(EXIT_FAILURE);
-  }
+	static struct option long_options[] = {
+		{"input", required_argument, 0, 'i'},
+		{"kmer",  required_argument, 0, 'k'},
+		{"nonzero", no_argument, 0, 'n'},
+		{"label", no_argument, 0, 'l'},
+		{"help", no_argument, 0, 'h'},
+		{0, 0, 0, 0}
+	};
 
-	unsigned long kmer = atoi(argv[2]);
-	unsigned long long width = pow_four(kmer);
+	while (1) {
 
+		int option_index = 0;
+		int c = 0;
+
+		c = getopt_long (argc, argv, "i:k:nlvh", long_options, &option_index);
+
+		if (c == -1)
+			break;
+
+		switch (c) {
+			case 'i':
+				filename = optarg;
+				break;
+			case 'k':
+				kmer = atoi(optarg);
+				kmer_set = true;
+				break;
+			case 'n':
+				nonzero = true; 
+				break;
+			case 'l':
+				label = true;
+				break;
+			case 'h':
+				printf("help-text\n");
+				exit(EXIT_SUCCESS);
+			default:
+				break;
+		}
+	}
+	if(filename == NULL) {
+		fprintf(stderr, "Error: filename (-i) must be supplied\n");
+		exit(EXIT_FAILURE);
+	}
+	if(kmer == NULL && !kmer_set) {
+		fprintf(stderr, "Error: kmer (-k) must be supplied\n");
+		exit(EXIT_FAILURE);
+	}
 	if(kmer == 0) { 
-		fprintf(stderr, "Error: invalid kmer.\n");
+		fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
 		exit(EXIT_FAILURE);
 	}
 
-	unsigned long long *counts = get_kmer_counts_from_file(argv[1], atoi(argv[2]));
+	width = pow_four(kmer);
+
+	unsigned long long *counts = get_kmer_counts_from_file(filename, kmer);
 
-	// print out our counts arrray
-	// manually unrolled 4 loops to reduce fprintf calls
-	if(argc == 3) {
+	// If nonzero is set, only print non zeros
+	if(nonzero) {
+		// if labels is set, print out our labels
+		if(label) {
+			for(i = 0; i < width; i++)
+				if(counts[i] != 0) 
+					fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer),i, counts[i]);
+				
+		}
+		else {
+			for(i = 0; i < width; i++)
+				if(counts[i] != 0) 
+					fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
+				
+		}
+	}
+	// If we aren't printing nonzeros print everything
+	else {
+		if(label) {
+			for(i = 0; i < width; i++)
+				fprintf(stdout, "%s\t%llu\n", index_to_kmer(i, kmer), counts[i]);
+		} 
+		else {
 		for(i = 0; i < width; i=i+4)
 			fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
-	} 
-	else {
-		for(i = 3; i < argc; i++) { 
-			unsigned long k = width;	
-			size_t len = 0;
-			fprintf(stdout, "%s\t", argv[i]);
-			
-			len = strlen(argv[i]);
-			if(len != kmer) { 
-				fprintf(stdout, "ERR\n");
-				continue;
-			}
-			for(j = 0; j < len; j++)
-				argv[i][j] = alpha[argv[i][j]];
-
-			k = num_to_index(argv[i], kmer, width);
-
-			if(k == width)  {
-				fprintf(stdout, "ERR\n");
-			}
-			else {
-				fprintf(stdout, "%llu\n", counts[k]);
-			}
 		}
 	}
 	return EXIT_SUCCESS;