From d8ca8e5bc9383255f32b23db8f702b941d65e340 Mon Sep 17 00:00:00 2001
From: Rob Long <robert.l.long@gmail.com>
Date: Fri, 7 Dec 2012 11:01:00 -0600
Subject: [PATCH 1/3] Remove original Makefile, update .gitignore, add
 CMakeLists.txt

---
 .gitignore     |  7 ++++++-
 CMakeLists.txt | 15 +++++++++++++++
 Makefile       | 19 -------------------
 3 files changed, 21 insertions(+), 20 deletions(-)
 create mode 100644 CMakeLists.txt
 delete mode 100644 Makefile

diff --git a/.gitignore b/.gitignore
index 9c2ec17..49f9f4b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,7 @@
 *.o
-fastahack
\ No newline at end of file
+fastahack
+libfastahack.a
+CMakeFiles
+CMakeCache.txt
+cmake_install.cmake
+Makefile
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..4727546
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,15 @@
+add_library(fastahck
+	FastaHack.cpp
+	Fasta.cpp
+	split.cpp
+	disorder.c
+)
+
+add_executable(fastahack
+	FastaHack.cpp
+	disorder.c
+)
+
+target_link_libraries(fastahack
+	fastahck
+)
diff --git a/Makefile b/Makefile
deleted file mode 100644
index b0d847e..0000000
--- a/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-CXX=g++
-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64
-
-fastahack: Fasta.o FastaHack.cpp split.o disorder.o
-	$(CXX) $(CFLAGS) Fasta.o FastaHack.cpp split.o disorder.o -o fastahack
-
-Fasta.o: Fasta.h Fasta.cpp
-	$(CXX) $(CFLAGS) -c Fasta.cpp
-
-split.o: split.h split.cpp
-	$(CXX) $(CFLAGS) -c split.cpp
-
-disorder.o: disorder.c disorder.h
-	$(CXX) $(CFLAGS) -c disorder.c
-
-clean:
-	rm -f fastahack *.o
-
-.PHONY: clean

From b6488c8083a6c06c5af6cd5e4edac0915feda1c1 Mon Sep 17 00:00:00 2001
From: Rob Long <robert.l.long@gmail.com>
Date: Fri, 7 Dec 2012 11:02:35 -0600
Subject: [PATCH 2/3] Specify disorder.c include as extern

---
 FastaHack.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/FastaHack.cpp b/FastaHack.cpp
index fac0963..b542abc 100644
--- a/FastaHack.cpp
+++ b/FastaHack.cpp
@@ -1,7 +1,9 @@
 #include "Fasta.h"
 #include <stdlib.h>
 #include <getopt.h>
+extern "C" {
 #include "disorder.h"
+}
 
 void printSummary() {
     cerr << "usage: fastahack [options] <fasta reference>" << endl

From 18b6b87207c3764c000a4e9dadbfa7e7d5dce8a3 Mon Sep 17 00:00:00 2001
From: Rob Long <robert.l.long@gmail.com>
Date: Fri, 7 Dec 2012 12:12:42 -0600
Subject: [PATCH 3/3] updated README and resolved a naming conflict in
 CMakeLists.txt

---
 CMakeLists.txt | 14 ++++++++++----
 README         |  9 +++++++++
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4727546..e556379 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,15 +1,21 @@
-add_library(fastahck
+cmake_minimum_required(VERSION 2.8)
+
+add_library(fastahack
 	FastaHack.cpp
 	Fasta.cpp
 	split.cpp
 	disorder.c
 )
 
-add_executable(fastahack
+add_executable(fastahack-bin
 	FastaHack.cpp
 	disorder.c
 )
 
-target_link_libraries(fastahack
-	fastahck
+set_target_properties(fastahack-bin
+	PROPERTIES OUTPUT_NAME fastahack
+)
+
+target_link_libraries(fastahack-bin
+	fastahack
 )
diff --git a/README b/README
index 5ccba37..7d82aa5 100644
--- a/README
+++ b/README
@@ -25,6 +25,15 @@ extraction without RAM-intensive file loading operations.  This makes fastahack
 a useful tool for bioinformaticists who need to quickly extract many
 subsequences from a reference FASTA sequence.
 
+Build:
+
+Cmake is required to build this project. Issue the following commands from the
+fastahack director:
+
+	% cmake .
+	% make
+	
+
 
 Notes: