Unbundle the included samtools and SeqAn, and use system libraries.
See also: https://bugs.gentoo.org/show_bug.cgi?id=566494

Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend
on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead.
See also: https://bugs.gentoo.org/show_bug.cgi?id=594810

--- a/configure.ac
+++ b/configure.ac
@@ -28,26 +28,15 @@
 AC_PROG_INSTALL
 AM_PATH_PYTHON([2.4])
 
-m4_include([ax_boost_base.m4])
-m4_include([ax_boost_thread.m4])
 # CXXFLAGS="$CXXFLAGS $threadLib"
 AX_BOOST_BASE([1.38.0])
+AX_BOOST_SYSTEM
 AX_BOOST_THREAD
-if test -z "$BOOST_THREAD_LIBS"; then
+if test -z "$BOOST_THREAD_LIB"; then
   AC_MSG_ERROR([boost.thread not found. Aborting.])
 fi
 
 
-# BAM related:
- ac_bam_path=samtools-0.1.18
- BAM_LIB="-lbam"
- BAM_LDFLAGS="-L./$ac_bam_path"
- BAM_CPPFLAGS="-I./$ac_bam_path"
- AC_SUBST(BAM_CPPFLAGS)
- AC_SUBST(BAM_LDFLAGS)
- AC_SUBST(BAM_LIB)
-
-
 # Checks for header files.
 AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
 
@@ -80,32 +69,23 @@
 # set CFLAGS and CXXFLAGS
 #user_CFLAGS="${CXXFLAGS}"
 user_CFLAGS=${CFLAGS}
-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
+generic_CFLAGS=""
 ext_CFLAGS=""
 debug_CFLAGS=""
 user_LDFLAGS="$LDFLAGS"
 
-AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
-			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
-
 AC_ARG_ENABLE([debug],
               [AS_HELP_STRING([--enable-debug],
 	                      [enable debugging info (default is no)])],
               [], [enable_debug=no])
-AC_ARG_ENABLE([optim],
-              [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
-	                      [set optimization level (default is 3)])],
-              [if test "x$enable_optim" = xyes; then enable_optim=3; fi],
-              [enable_optim=3])
 
-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])	
 AS_IF([test "x$enable_debug" = xyes],
       [debug_CFLAGS="-DDEBUG"],
       [debug_CFLAGS="-DNDEBUG"])
 	  
 CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
 CXXFLAGS="$CFLAGS"
-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
+CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
 LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
 
 AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
@@ -122,7 +102,7 @@
 -- ${PACKAGE_STRING} Configuration Results --
   C++ compiler:        ${CXX} ${CXXFLAGS}
   Linker flags:        ${LDFLAGS}
-  BOOST libraries:     ${BOOST_THREAD_LIBS}"
+  BOOST libraries:     ${BOOST_THREAD_LIB}"
 
 if test x"${GCC}" = x"yes" ; then
    gcc_version=`${CC} --version | head -n 1`
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -683,17 +683,12 @@
 SeqAn-1.4.2/seqan/system/system_thread.h \
 SeqAn-1.4.2/seqan/version.h
 
-SAMDIR = ./samtools-0.1.18
-SAMLIB = libbam.a
-SAMPROG = samtools_0.1.18
-BAM_LIB = -lbam
-BAM_CPPFLAGS = -I$(SAMDIR)
-BAM_LDFLAGS = -L$(SAMDIR)
+BAM_LIB = -lbam-0.1-legacy
+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/
 
 #-- progs to be installed in $prefix/bin
 
 bin_PROGRAMS = \
-	$(SAMPROG) \
 	prep_reads \
 	gtf_to_fasta \
 	fix_map_ordering \
@@ -722,9 +717,6 @@
 	tophat2 \
 	tophat
 
-clean-local:
-	cd $(SAMDIR) && make clean
-
 tophat2: tophat2.sh
 	cp tophat2.sh tophat2 && chmod 755 tophat2
 
@@ -732,7 +724,7 @@
 	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
 
 #-- tophat library for linking convienence
-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
+noinst_LIBRARIES = libgc.a libtophat.a
 
 noinst_HEADERS = \
 	reads.h \
@@ -801,11 +793,11 @@
 prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) 
 
 segment_juncs_SOURCES = segment_juncs.cpp
-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
 segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
 
 long_spanning_reads_SOURCES = long_spanning_reads.cpp
-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
 long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
 
 gtf_juncs_SOURCES = gtf_juncs.cpp
@@ -817,7 +809,7 @@
 juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
 
 tophat_reports_SOURCES = tophat_reports.cpp
-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
 tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
 
 fix_map_ordering_SOURCES = fix_map_ordering.cpp
@@ -844,15 +836,5 @@
 gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
 gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
 
-
-libbam_a_SOURCES = 
-samtools_0_1_18_SOURCES = 
-
-$(SAMPROG): $(SAMLIB)
-	
-
-$(SAMLIB):
-	cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
-
 install-data-hook:
 	cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)