From 9769350e545f44d19f0a3c676ced157b5e76cd36 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 4 Mar 2014 15:26:20 -0500
Subject: rework makefile

---
 Makefile | 20 +++++++++-----------
 sparse.c | 62 --------------------------------------------------------------
 sparse.h | 17 -----------------
 3 files changed, 9 insertions(+), 90 deletions(-)
 delete mode 100644 sparse.c
 delete mode 100644 sparse.h

diff --git a/Makefile b/Makefile
index 61bde0e..bc90a64 100644
--- a/Makefile
+++ b/Makefile
@@ -4,21 +4,19 @@ CFLAGS = -O3 -s -mtune=native -Wall -Wextra -DVERSION=$(VERSION) -std=c++11
 DESTDIR = /usr/local/
 
 
-all: libkmer.o libkmer.so kmer_total_count kmer_counts_per_sequence
+all: kmer_utils.o libkmer.so kmer_total_count kmer_counts_per_sequence
 
-sparse.o: sparse.c
-	$(CC) -c sparse.c -o sparse.o $(CFLAGS) 
-libkmer.o: kmer_utils.c
-	$(CC) -c kmer_utils.c -o libkmer.o $(CFLAGS) -fPIC
-libkmer.so: libkmer.o
+kmer_utils.o: kmer_utils.c
+	$(CC) -c kmer_utils.c -o kmer_utils.o $(CFLAGS) -fPIC
+libkmer.so: kmer_utils.o
 	$(CC) kmer_utils.c -o libkmer.so $(CFLAGS) -shared -fPIC
-kmer_total_count: kmer_utils.c kmer_total_count.c kmer_utils.h
-	$(CC) kmer_utils.c kmer_total_count.c -o kmer_total_count $(CLIBS) $(CFLAGS)
-kmer_counts_per_sequence: libkmer.o kmer_counts_per_sequence.c kmer_utils.h
-	$(CC) libkmer.o kmer_counts_per_sequence.c -o kmer_counts_per_sequence $(CLIBS) $(CFLAGS)
+kmer_total_count: kmer_utils.o kmer_total_count.c kmer_utils.h
+	$(CC) kmer_utils.o kmer_total_count.c -o kmer_total_count $(CLIBS) $(CFLAGS)
+kmer_counts_per_sequence: kmer_utils.o kmer_counts_per_sequence.c kmer_utils.h
+	$(CC) kmer_utils.o kmer_counts_per_sequence.c -o kmer_counts_per_sequence $(CLIBS) $(CFLAGS)
 
 clean:
-	rm -vf kmer_total_count kmer_counts_per_sequence libkmer.so libkmer.o
+	rm -vf kmer_total_count kmer_counts_per_sequence kmer_utils.o libkmer.so
 
 debug: CFLAGS = -ggdb -Wall -Wextra -DVERSION=$(VERSION)\"-debug\"
 debug: all
diff --git a/sparse.c b/sparse.c
deleted file mode 100644
index 30ce2b1..0000000
--- a/sparse.c
+++ /dev/null
@@ -1,62 +0,0 @@
-#include <errno.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdbool.h>
-
-struct bin_tree {
-	size_t index;
-	unsigned long long value;
-	struct bin_tree *right;
-	struct bin_tree *left;
-};
-
-typedef struct bin_tree node;
-
-void insert(node ** tree, size_t index) {
-	node *temp = NULL;
-	if(!(*tree)) {
-		temp = (node *)malloc(sizeof(node));
-		temp->left = temp->right = NULL;
-		temp->index = index;
-		temp->value = 1;
-		*tree = temp;
-		return;
-	}
-
-	if(index < (*tree)->index)
-		insert(&(*tree)->left, index);
-	else if(index > (*tree)->index)
-		insert(&(*tree)->right, index);
-
-}
-
-void deltree(node * tree) {
-	if (tree) {
-		deltree(tree->left);
-		deltree(tree->right);
-		free(tree);
-	}
-}
-
-node* search(node ** tree, size_t index) {
-	if(!(*tree))
-		return NULL;
-
-	if(index < (*tree)->index)
-		search(&((*tree)->left), index);
-
-	else if(index > (*tree)->index)
-		search(&((*tree)->right), index);
-
-	else if(index == (*tree)->index)
-		return *tree;
-}
-
-unsigned long long *lookup(node **tree, size_t index) {
-	node *ret = search(tree, index);
-	if(ret)
-		return ret->value;
-	else
-		return 0;
-}
diff --git a/sparse.h b/sparse.h
deleted file mode 100644
index 2ffbabd..0000000
--- a/sparse.h
+++ /dev/null
@@ -1,17 +0,0 @@
-#include <stdbool.h>
-
-struct b_tree {
-	size_t index;
-	unsigned long long value;
-	struct b_tree *right;
-	struct b_tree *left;
-};
-
-typedef struct b_tree node;
-
-node* search(node **tree, size_t index);
-void insert(node **tree, size_t index);
-void deltree(node *tree);
-unsigned long long lookup(node **tree, size_t index);
-
-void print_sparse(node *tree, bool label, bool nonzero, unsigned int kmer);
-- 
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