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Modify the buildsystem to work with the legacy version of samtools,
which can coexist with the most recent version of samtools.
See also: https://bugs.gentoo.org/show_bug.cgi?id=577854
--- cufflinks-2.2.1/ax_bam.m4
+++ cufflinks-2.2.1/ax_bam.m4
@@ -102,7 +102,7 @@
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <bam/bam.h>
+ @%:@include <bam-0.1-legacy/bam.h>
]], [[
]])],[
AC_MSG_RESULT(yes)
@@ -171,7 +171,7 @@
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <bam/version.hpp>
+ @%:@include <bam-0.1-legacy/version.hpp>
]], [[
]])],[
AC_MSG_RESULT(yes)
@@ -189,7 +189,7 @@
AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
fi
else
- BAM_LIB="-lbam"
+ BAM_LIB="-lbam-0.1-legacy"
AC_SUBST(BAM_CPPFLAGS)
AC_SUBST(BAM_LDFLAGS)
AC_SUBST(BAM_LIB)
--- cufflinks-2.2.1/src/hits.h
+++ cufflinks-2.2.1/src/hits.h
@@ -18,7 +18,7 @@
#include <boost/shared_ptr.hpp>
-#include <bam/sam.h>
+#include <bam-0.1-legacy/sam.h>
#include "common.h"
#include "multireads.h"
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