Clean up indentation and whitespace

1 files changed, 111 insertions, 116 deletions

diff --git a/kmer_total_count.c b/kmer_total_count.c
index 5ce7ee1..5dbb50d 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -9,121 +9,116 @@
 #include "kmer_utils.h"
 
 int main(int argc, char **argv) {
-
-
-	char *filename = NULL;
-        FILE *fh;
-
-	unsigned int kmer = 0;
-
-	bool nonzero = 0;
-	bool label = 0;
-	bool kmer_set = 0;
-
-	unsigned long long width = 0;
-
-	unsigned long long i = 0;
-
-	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}
-	};
-
-	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 == 0 && !kmer_set) {
-		fprintf(stderr, "Error: kmer (-k) must be supplied\n");
-		exit(EXIT_FAILURE);
-	}
-	if(kmer == 0) { 
-		fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
-		exit(EXIT_FAILURE);
-	}
-
-        fh = fopen(filename, "r");
-        if(fh == NULL) {
-          fprintf(stderr, "Could not open %s\n", filename);
-          exit(EXIT_FAILURE);
+  char *filename = NULL;
+  FILE *fh;
+
+  unsigned int kmer = 0;
+
+  bool nonzero = 0;
+  bool label = 0;
+  bool kmer_set = 0;
+
+  unsigned long long width = 0;
+
+  unsigned long long i = 0;
+
+  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}
+  };
+
+  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 == 0 && !kmer_set) {
+    fprintf(stderr, "Error: kmer (-k) must be supplied\n");
+    exit(EXIT_FAILURE);
+  }
+  if(kmer == 0) {
+    fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
+    exit(EXIT_FAILURE);
+  }
+
+  fh = fopen(filename, "r");
+  if(fh == NULL) {
+    fprintf(stderr, "Could not open %s\n", filename);
+    exit(EXIT_FAILURE);
+  }
+
+  width = pow_four(kmer);
+
+  unsigned long long *counts = get_kmer_counts_from_file(fh, kmer);
+
+  // 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) {
+          char *kmer_str = index_to_kmer(i, kmer);
+          fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+          free(kmer_str);
         }
-
-	width = pow_four(kmer);
-
-	unsigned long long *counts = get_kmer_counts_from_file(fh, kmer);
-
-	// 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) {
-					char *kmer_str = index_to_kmer(i, kmer);
-					fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
-					free(kmer_str);
-				}
-
-		}
-		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++) {
-				if(counts[i] != 0) {
-					char *kmer_str = index_to_kmer(i, kmer);
-					fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
-					free(kmer_str);
-				}
-			} 
-		}
-		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]);
-			}
-		}
-	}
-
-	free(counts);
-	return EXIT_SUCCESS;
+    }
+    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++) {
+        if(counts[i] != 0) {
+          char *kmer_str = index_to_kmer(i, kmer);
+          fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
+          free(kmer_str);
+        }
+      }
+    }
+    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]);
+      }
+    }
+  }
+
+  free(counts);
+  return EXIT_SUCCESS;
 }