Initial commit of some kmer utilities.

there are two utilties included.

one is kmer_frequency_per_sequence,
which outputs a (m x n) matrix where m is the sequence, and n is the
frequency of that nmer to occur in the given sequence.

the other tool is kmer_total_count, which counts kmers for the total
file, not just one sequence

1 files changed, 54 insertions, 0 deletions

diff --git a/kmer_utils.c b/kmer_utils.c
new file mode 100644
index 0000000..b6f66b5
--- /dev/null
+++ b/kmer_utils.c
@@ -0,0 +1,54 @@
+#include <stdint.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+// This function takes a char array containing sequences and converts it
+// into a kmer index (essentially a base 4 radix converstion to base 10, with
+// some mumbo-jumbo of taking each of the characters we want (ACGT) and turning
+// them into a radix-4 number we can use.
+//
+// kind of convoluted but it works.
+//
+// Arguemnts: 
+//  char *str - a NULL terminated character array 
+//  long kmer - how long of a index value you want to return
+//  long error_pos - what index to return for a non ACGT character
+//
+long convert_kmer_to_index(char *str, long kmer, long error_pos) {
+
+  char **ptr = NULL;
+  char vals[kmer];
+  long i = 0;
+  long ret = 0;
+
+  for(i = 0; i < kmer; i++) {
+    int val = 0;
+    switch(str[i]) {
+      case 'a':
+      case 'A':
+        val = 48;
+        break;
+      case 'c':
+      case 'C':
+        val = 49;
+        break;
+      case 'g':
+      case 'G':
+        val = 50;
+        break;
+      case 't':
+      case 'T':
+        val = 51;
+        break;
+      default:
+        return error_pos; 
+    }
+
+
+    vals[i] = val; 
+  }
+
+  ret = strtol(vals, ptr, 4);
+  return ret;
+}