From f47ce6202d2bb6425638a9142bbbebd7d44fb64f Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 2 Oct 2013 21:38:43 -0400
Subject: use an external iterator so that we can skip over anything in range
 of an errorw

---
 Makefile                      |  2 +-
 kmer_frequency_per_sequence.c |  5 ++---
 kmer_frequency_per_sequence.h |  1 +
 kmer_total_count.c            |  9 ++++-----
 kmer_total_count.h            |  1 +
 kmer_utils.c                  | 13 ++++++++++---
 kmer_utils.h                  |  2 +-
 7 files changed, 20 insertions(+), 13 deletions(-)
 create mode 100644 kmer_frequency_per_sequence.h
 create mode 100644 kmer_total_count.h

diff --git a/Makefile b/Makefile
index a009094..55b4805 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ CFLAGS = -O3 -s -mtune=native -Wall -lm -DVERSION=$(VERSION) -Wextra
 all: libkmer.so kmer_total_count kmer_frequency_per_sequence
 
 libkmer.so:
-	$(CC) kmer_utils.c -o libkmer.so $(CFLAGS) -shared -FPIC
+	$(CC) kmer_utils.c -o libkmer.so $(CFLAGS) -shared -FPIC -DSHARED=0
 kmer_total_count:
 	$(CC) kmer_total_count.c kmer_utils.c -o kmer_total_count $(CFLAGS)
 kmer_frequency_per_sequence:
diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
index ae15bd2..9cda533 100644
--- a/kmer_frequency_per_sequence.c
+++ b/kmer_frequency_per_sequence.c
@@ -1,13 +1,12 @@
 // Copyright 2013 Calvin Morrison
 #include <math.h>
-#include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
 
 #include "kmer_utils.h"
 
+long position = 0;
+
 int main(int argc, char **argv) {
 
   char *line = NULL;
diff --git a/kmer_frequency_per_sequence.h b/kmer_frequency_per_sequence.h
new file mode 100644
index 0000000..e782906
--- /dev/null
+++ b/kmer_frequency_per_sequence.h
@@ -0,0 +1 @@
+extern long position;
diff --git a/kmer_total_count.c b/kmer_total_count.c
index 3a418ed..e953d88 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -1,13 +1,12 @@
 // Copyright 2013 Calvin Morrison
 #include <math.h>
-#include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
 
 #include "kmer_utils.h"
 
+long position = 0;
+
 int main(int argc, char **argv) {
 
   char *line = NULL;
@@ -43,8 +42,8 @@ int main(int argc, char **argv) {
     if(line[0] != '>' && read > kmer) {
       convert_kmer_to_num(line, read);
 
-      for(i = 0; i < (read - kmer); i++) {
-        counts[num_to_index(&line[i],kmer, width)]++;
+      for(position = 0; position < (read - kmer); position++) {
+        counts[num_to_index(&line[position],kmer, width)]++;
       }
     } 
   }
diff --git a/kmer_total_count.h b/kmer_total_count.h
new file mode 100644
index 0000000..e782906
--- /dev/null
+++ b/kmer_total_count.h
@@ -0,0 +1 @@
+extern long position;
diff --git a/kmer_utils.c b/kmer_utils.c
index f63caef..f4f8d2f 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -1,6 +1,8 @@
+#include "kmer_total_count.h"
+
 // convert a string of k-mer size base-4 values  into a
 // base-10 index
-long num_to_index(const char *str, const int kmer, const long error_pos) {
+unsigned long num_to_index(const char *str, const int kmer, const long error_pos) {
 
   int i = 0;
   unsigned long out = 0;
@@ -8,8 +10,13 @@ long num_to_index(const char *str, const int kmer, const long error_pos) {
 
   for(i = kmer - 1; i >= 0; i--){
 
-    if(str[i] >> 2)
-      return error_pos;
+		if(str[i] >> 2) { 
+			#ifndef SHARED
+			position += i;
+			#endif
+			return error_pos;
+		}
+
 
     out += str[i] * multiply;
     multiply = multiply << 2;
diff --git a/kmer_utils.h b/kmer_utils.h
index b7bfb1a..f1a84b6 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,2 +1,2 @@
 void convert_kmer_to_num(char *str, const unsigned long length);
-long num_to_index(const char *str, const int kmer, const long error_pos);
+unsigned long num_to_index(const char *str, const int kmer, const long error_pos);
-- 
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