Author: Sascha Steinbiss <sascha@steinbiss.name>
Description: use shared libraries
--- a/makefile
+++ b/makefile
@@ -7,7 +7,7 @@
 
 CC 	= g++
 CFLAGS	= -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
-CLINK	= -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
+CLINK	= -lm -lz -lbz2 -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
 
 DISABLE_ASMLIB = true
 
@@ -25,10 +25,6 @@
 $(KMC_MAIN_DIR)/kb_storer.o \
 $(KMC_MAIN_DIR)/kmer.o
 
-KMC_LIBS = \
-$(KMC_MAIN_DIR)/libs/libz.a \
-$(KMC_MAIN_DIR)/libs/libbz2.a
-
 KMC_DUMP_OBJS = \
 $(KMC_DUMP_DIR)/nc_utils.o \
 $(KMC_API_DIR)/mmer.o \
@@ -51,7 +47,7 @@
 
 kmc: $(KMC_OBJS)
 	-mkdir -p $(KMC_BIN_DIR)
-	$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^ $(KMC_LIBS)
+	$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
 kmc_dump: $(KMC_DUMP_OBJS)
 	-mkdir -p $(KMC_BIN_DIR)
 	$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
--- a/kmer_counter/fastq_reader.h
+++ b/kmer_counter/fastq_reader.h
@@ -16,8 +16,8 @@
 #include <stdio.h>
 #include <iostream>
 
-#include "libs/zlib.h"
-#include "libs/bzlib.h"
+#include <zlib.h>
+#include <bzlib.h>
 
 
 using namespace std;
@@ -42,10 +42,10 @@
 	int bzerror;
 
 	uint64 part_size;
-	
+
 	uchar *part;
 	uint64 part_filled;
-	
+
 	uint32 gzip_buffer_size;
 	uint32 bzip2_buffer_size;
 
