From 961e322676c3c3e623c2a116a9a049134d4f51d9 Mon Sep 17 00:00:00 2001
From: Jeremiah Wala <jwala@broadinstitute.org>
Date: Thu, 18 Jun 2015 13:27:18 -0400
Subject: [PATCH] updated build

---
 src/GenomicRegionCollection.cpp | 7 +++++++
 src/config.status               | 6 +++---
 src/configure                   | 3 +--
 src/configure.ac                | 4 ++--
 4 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/GenomicRegionCollection.cpp b/src/GenomicRegionCollection.cpp
index 52f3232e3..59b01d435 100644
--- a/src/GenomicRegionCollection.cpp
+++ b/src/GenomicRegionCollection.cpp
@@ -415,6 +415,8 @@ template<class T>
 GRC GenomicRegionCollection<T>::complement(GRC& subject, bool ignore_strand)
 {
   
+#ifdef BOOST_CONFIG_HPP
+
   GRC out;
   // get this - that
 
@@ -459,6 +461,11 @@ GRC GenomicRegionCollection<T>::complement(GRC& subject, bool ignore_strand)
 
   return out;
 
+#else
+  std::cerr << "No Boost library detected. GenomicRegionCollection::complement will not function. Returning Empty GRC"
+    return GRC();
+#endif
+
 }
 
 template<class T>
diff --git a/src/config.status b/src/config.status
index f4849cdf6..f173716db 100755
--- a/src/config.status
+++ b/src/config.status
@@ -298,7 +298,7 @@ Report bugs to <bug-autoconf@gnu.org>."
 ac_cs_version="\
 snowtools config.status 1.0
 configured by ./configure, generated by GNU Autoconf 2.59,
-  with options \"\"
+  with options \"'--with-boost=asdf'\"
 
 Copyright (C) 2003 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
@@ -377,8 +377,8 @@ if $ac_cs_silent; then
 fi
 
 if $ac_cs_recheck; then
-  echo "running /bin/sh ./configure "  $ac_configure_extra_args " --no-create --no-recursion" >&6
-  exec /bin/sh ./configure  $ac_configure_extra_args --no-create --no-recursion
+  echo "running /bin/sh ./configure " '--with-boost=asdf' $ac_configure_extra_args " --no-create --no-recursion" >&6
+  exec /bin/sh ./configure '--with-boost=asdf' $ac_configure_extra_args --no-create --no-recursion
 fi
 
 #
diff --git a/src/configure b/src/configure
index f2cfd98d0..3cdba5d9e 100755
--- a/src/configure
+++ b/src/configure
@@ -865,8 +865,7 @@ Optional Features:
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
-  --with-boost=PATH       specify directory containing the bamtools library
-                          (http://github.com/pezmaster31/bamtools)
+  --with-boost=PATH       specify directory containing the boost library)
 
 Some influential environment variables:
   CXX         C++ compiler command
diff --git a/src/configure.ac b/src/configure.ac
index 0f758778b..281280736 100644
--- a/src/configure.ac
+++ b/src/configure.ac
@@ -21,11 +21,11 @@ AC_SEARCH_LIBS([gzopen],[z],,[AC_MSG_ERROR([libz not found, please install zlib
 AC_SEARCH_LIBS([clock_gettime], [rt], [AC_DEFINE([HAVE_CLOCK_GETTIME], [1], [clock_getttime found])], )
 
 AC_ARG_WITH(boost, AS_HELP_STRING([--with-boost=PATH],
-	[specify directory containing the bamtools library (http://github.com/pezmaster31/bamtools)]))
+	[specify directory containing the boost library)]))
 if test "$with_boost" -a -d "$with_boost"; then
     boost_include="-I$with_boost"
 else
-    boostr=/xchip/gistic/Jeremiah/boost_1_58_0
+    boostr=/xchip/gistic/Jeremiah/boost_1_58_0DUMY
     boost_include="-I$boostr"
 fi