standard build using GNU autotools

.gitignore

@@ -1,2 +1,35 @@
+# http://www.gnu.org/software/autoconf
+
+/autom4te.cache
+/aclocal.m4
+/compile
+/configure
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+/test-driver
+/INSTALL
+
+# http://www.gnu.org/software/automake
+
+Makefile.in
+
+# autoscan
+
+/autoscan.log
+/configure.scan
+/config.h.in
+
+# configure
+
+Makefile
+/config.h
+/config.log
+/config.status
+.deps
+
+# make
+
 *.o
 sickle

Makefile.am

@@ -0,0 +1,2 @@
+SUBDIRS = src test
+EXTRA_DIST = sickle.xml

README.md

@@ -53,7 +53,8 @@ Sickle doesn't have a paper, but you can cite it like this:
 ## Requirements 
 
 Sickle requires a C compiler; GCC or clang are recommended. Sickle
-relies on Heng Li's kseq.h, which is bundled with the source.
+relies on Heng Li's kseq.h, which is provided by
+[htslib](https://github.com/samtools/htslib/).
 
 Sickle also requires Zlib, which can be obtained at
 <http://www.zlib.net/>.
@@ -62,9 +63,14 @@ Sickle also requires Zlib, which can be obtained at
 
 To build Sickle, enter:
 
+    ./configure
     make
+    make install
 
-Then, copy or move "sickle" to a directory in your $PATH.
+In case configure is not included in your distribution, e.g. when cloning the
+source from github, run the following first:
+
+    ./bootstrap
 
 ## Usage
 

bootstrap

@@ -0,0 +1 @@
+autoreconf -i

configure.ac

@@ -0,0 +1,31 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.69])
+AC_INIT([sickle], [1.33], [https://github.com/najoshi/sickle/issues])
+AC_CONFIG_SRCDIR([config.h.in])
+AC_CONFIG_HEADERS([config.h])
+
+AM_INIT_AUTOMAKE([foreign])
+
+# Checks for programs.
+AC_PROG_CC
+
+# Checks for libraries.
+PKG_CHECK_MODULES(HTSLIB, htslib)
+PKG_CHECK_MODULES(ZLIB, zlib)
+
+# Checks for header files.
+AC_CHECK_HEADERS([limits.h stdlib.h string.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_CHECK_FUNCS([strstr])
+
+AC_CONFIG_FILES([Makefile
+                 src/Makefile
+                 test/Makefile])
+
+AC_OUTPUT

src/Makefile.am

@@ -0,0 +1,8 @@
+AM_CFLAGS = -Wall -pedantic -O3
+
+bin_PROGRAMS = sickle
+
+sickle_SOURCES = print_record.c print_record.h sickle.c sickle.h sliding.c trim_paired.c trim_single.c
+
+sickle_CPPFLAGS = $(HTSLIB_CPPFLAGS) $(ZLIB_CPPFLAGS)
+sickle_LDADD = $(ZLIB_LIBS)

src/print_record.c

@@ -1,11 +1,12 @@
 #include <assert.h>
 #include <ctype.h>
 #include <stdlib.h>
+#include <stdint.h>
 #include <zlib.h>
 #include <stdio.h>
 #include <unistd.h>
 #include "sickle.h"
-#include "kseq.h"
+#include <htslib/kseq.h>
 
 
 void print_record (FILE *fp, kseq_t *fqr, cutsites *cs) {