Merge branch 'master' of github.com:mutantturkey/quikr

1 files changed, 0 insertions, 153 deletions

diff --git a/src/c/quikr_functions.c.1 b/src/c/quikr_functions.c.1
deleted file mode 100644
index 31afb3b..0000000
--- a/src/c/quikr_functions.c.1
+++ /dev/null
@@ -1,153 +0,0 @@
-#include <stdio.h>
-#include <stdio.h>
-#include <errno.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <string.h>
-#include <math.h>
-#include <zlib.h>
-
-int count_sequences(char *filename) { 
-  char command[512];
-  int sequences = 0;
-  FILE *grep_output;
-
-  sprintf(command, "grep -c ^\\> %s", filename);
-  grep_output = popen(command, "r");
-  if(grep_output == NULL) {
-    fprintf(stderr, "Could not execute %s\n", command);
-    exit(EXIT_FAILURE);
-  }
-  
-  fscanf(grep_output, "%d", &sequences);
-
-  pclose(grep_output);
-  return sequences;
-}
-
-
-void normalize_matrix(double *matrix, int height, int width) {
-  int x = 0;
-  int y = 0;
-  for(x = 0; x < height; x++) {
-
-    double row_sum = 0;
-
-    for(y = 0; y < (width); y++)
-      row_sum = row_sum + matrix[width * x + y];
-    for(y = 0; y < (width); y++) 
-      matrix[width * x + y] = matrix[width * x + y] / row_sum; 
-  }
-}
-
-
-double *load_count_matrix(char *filename, int width, int kmer) {
-
-  double *count_matrix = malloc((width)*sizeof(double));
-  char count_command[512];
-  int x = 0;
-  char *line = NULL;
-  size_t len = 0;
-
-  if(count_matrix == NULL) {
-    fprintf(stderr, "could not allocate enough memory for the count matrix (%d x double) \n", width);
-    exit(EXIT_FAILURE);
-  }
-
-  // create out count matrix
-  sprintf(count_command, "count-kmers -r %d -1 -u %s", kmer, filename);
-  FILE *count_output = popen(count_command, "r");
-  if(count_output == NULL) {
-    fprintf(stderr, "could not execute \"%s\"", count_command);
-    exit(EXIT_FAILURE);
-  }
-
-  // set first element to zero.
-  count_matrix[0] = 0;
-
-  // get our first line
-  getline(&line, &len, count_output);
-  count_matrix[1] = atoi(line);
-
-  // iterate over the rest of the lines
-  for(x = 2; x < width; x++) { 
-    getline(&line, &len, count_output);
-    count_matrix[x] = atoi(line);
-  } 
-
-  pclose(count_output);
-
-  return count_matrix;
-}
-
-
-double *load_sensing_matrix(char *filename, int height, int width) {
-
-  int x = 0;
-  int y = 0;
-
-  gzFile sensing_matrix_fh = NULL;
-
-  double *sensing_matrix = malloc(height * width * sizeof(double));
-  if(sensing_matrix == NULL) {
-    fprintf(stderr, "Could not allocate memory for the sensing matrix\n");
-  }
-
-  sensing_matrix_fh = gzopen(filename, "r");
-  if(sensing_matrix_fh == NULL) {
-    fprintf(stderr, "could not open %s", filename);
-    exit(EXIT_FAILURE);
-  }
-
-  // read our sensing matrix in
-  for(x = 0; x < height; x++) {
-    for (y = 1; y < width; y++) {
-      char buffer[14];
-      gzgets(sensing_matrix_fh, buffer, 14); 
-      sensing_matrix[width*x + y] = atof(buffer);
-    }
-  }
-
-  gzclose(sensing_matrix_fh);
-
-  return sensing_matrix;
-}
-
-char **load_headers(char *filename, int sequences) {
-  char command[512];
-  char *line= NULL;
-  int x = 0;
-  FILE *grep_output;
-  size_t len = 0;
-
-  sprintf(command, "grep ^\\> %s", filename);
-  grep_output = popen(command, "r");
-  if(grep_output == NULL) {
-    fprintf(stderr, "Could not execute %s\n", command);
-    exit(EXIT_FAILURE);
-  }
-  
-  char **headers = malloc(sequences * sizeof(char *));
-  if(headers == NULL) {
-    fprintf(stderr, "could not allocated enough memory\n");
-    exit(EXIT_FAILURE);
-  }
-
-  for(x = 0; x < sequences; x++) {
-
-    char *header = malloc(256 * sizeof(char));
-    if(header == NULL) {
-      fprintf(stderr, "could not allocated enough memory\n");
-      exit(EXIT_FAILURE);
-    }
-    getline(&line, &len, grep_output);
-    sscanf(line + 1, "%s", header);
-    headers[x] = header;
-  }
-
-  pclose(grep_output);
-
-  return headers;
-}
-