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

--- tophat-2.1.1/configure.ac
+++ tophat-2.1.1/configure.ac
@@ -38,16 +38,6 @@
 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 +70,23 @@
 # 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])
--- tophat-2.1.1/src/Makefile.am
+++ tophat-2.1.1/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 \
@@ -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)