updated build

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>

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
 
 #

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

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