diff options
| -rw-r--r-- | Makefile | 20 | ||||
| -rw-r--r-- | sparse.c | 62 | ||||
| -rw-r--r-- | sparse.h | 17 |
3 files changed, 9 insertions, 90 deletions
@@ -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); |