361 lines
15 KiB
Diff
361 lines
15 KiB
Diff
From d94b8582e580f7c110b64705b79aa6ae3748f0d1 Mon Sep 17 00:00:00 2001
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From: zhangxianting <zhangxianting@uniontech.com>
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Date: Wed, 10 Apr 2024 14:37:17 +0800
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Subject: [PATCH 1/2] hts instead of bam , because samtools upgrade, remove /usr/lib64/libbam.a
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copy ax_hts.m4, base ax_bam.m4
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---
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ax_hts.m4 | 203 ++++++++++++++++++++++++++++
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configure.ac | 6 +-
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cufflinks.xcodeproj/project.pbxproj | 2 +-
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make_bin.sh | 8 +-
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src/Makefile.am | 32 ++---
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5 files changed, 227 insertions(+), 24 deletions(-)
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create mode 100644 ax_hts.m4
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diff --git a/ax_hts.m4 b/ax_hts.m4
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new file mode 100644
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index 0000000..b5f7e78
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--- /dev/null
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+++ b/ax_hts.m4
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@@ -0,0 +1,203 @@
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+# SYNOPSIS
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+#
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+# AX_HTS
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+#
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+# DESCRIPTION
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+#
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+# Test for the HTS libraries of a particular version (or newer)
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+#
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+# If no path to the installed hts library is given the macro searchs
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+# under /usr, /usr/local, /opt and /opt/local and evaluates the
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+# $HTS_ROOT environment variable.
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+# Adapted from AX_BOOST_BASE
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+#
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+# This macro calls:
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+#
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+# AC_SUBST(HTS_CPPFLAGS) / AC_SUBST(HTS_LDFLAGS)
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+#
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+# And sets:
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+#
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+# HAVE_HTS
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+#
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+# LICENSE
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+#
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+# Copyright (c) 2010 Cole Trapnell <cole@cs.umd.edu>
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+#
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+# Copying and distribution of this file, with or without modification, are
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+# permitted in any medium without royalty provided the copyright notice
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+# and this notice are preserved.
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+
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+AC_DEFUN([AX_HTS],
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+[
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+AC_ARG_WITH([hts],
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+ AS_HELP_STRING([--with-hts@<:@=DIR@:>@], [use HTS libraries (default is yes) - it is possible to specify the root directory for HTS (optional)]),
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+ [
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+ if test "$withval" = "no"; then
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+ want_hts="no"
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+ elif test "$withval" = "yes"; then
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+ want_hts="yes"
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+ ac_hts_path=""
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+ else
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+ want_hts="yes"
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+ ac_hts_path="$withval"
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+ fi
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+ ],
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+ [want_hts="yes"])
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+
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+
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+AC_ARG_WITH([hts-libdir],
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+ AS_HELP_STRING([--with-hts-libdir=LIB_DIR],
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+ [Force given directory for hts libraries. Note that this will overwrite library path detection, so use this parameter only if default library detection fails and you know exactly where your hts libraries are located.]),
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+ [
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+ if test -d $withval
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+ then
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+ ac_hts_lib_path="$withval"
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+ else
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+ AC_MSG_ERROR(--with-hts-libdir expected directory name)
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+ fi
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+ ],
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+ [ac_hts_lib_path=""]
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+)
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+
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+if test "x$want_hts" = "xyes"; then
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+# hts_lib_version_req=ifelse([$1], ,1.20.0,$1)
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+# hts_lib_version_req_shorten=`expr $hts_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
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+# hts_lib_version_req_major=`expr $hts_lib_version_req : '\([[0-9]]*\)'`
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+# hts_lib_version_req_minor=`expr $hts_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
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+# hts_lib_version_req_sub_minor=`expr $hts_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
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+# if test "x$hts_lib_version_req_sub_minor" = "x" ; then
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+# hts_lib_version_req_sub_minor="0"
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+# fi
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+# WANT_HTS_VERSION=`expr $htslib_version_req_major \* 100000 \+ $hts_lib_version_req_minor \* 100 \+ $hts_lib_version_req_sub_minor`
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+ AC_MSG_CHECKING(for htslib)
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+ succeeded=no
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+
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+ dnl first we check the system location for hts libraries
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+ if test "$ac_hts_path" != ""; then
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+ HTS_LDFLAGS="-L$ac_hts_path/lib"
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+ HTS_CPPFLAGS="-I$ac_hts_path/include"
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+ else
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+ for ac_hts_path_tmp in /usr /usr/local /opt /opt/local ; do
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+ if test -d "$ac_hts_path_tmp/include/htslib" && test -r "$ac_hts_path_tmp/include/htslib"; then
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+ HTS_LDFLAGS="-L$ac_hts_path_tmp/lib"
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+ HTS_CPPFLAGS="-I$ac_hts_path_tmp/include"
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+ break;
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+ fi
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+ done
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+ fi
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+
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+ dnl overwrite ld flags if we have required special directory with
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+ dnl --with-hts-libdir parameter
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+ if test "$ac_hts_lib_path" != ""; then
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+ HTS_LDFLAGS="-L$ac_hts_lib_path"
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+ fi
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+
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+ CPPFLAGS_SAVED="$CPPFLAGS"
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+ CPPFLAGS="$CPPFLAGS $HTS_CPPFLAGS"
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+ export CPPFLAGS
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+
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+ LDFLAGS_SAVED="$LDFLAGS"
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+ LDFLAGS="$LDFLAGS $HTS_LDFLAGS"
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+ export LDFLAGS
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+
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+ AC_LANG_PUSH(C++)
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+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
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+ @%:@include <htslib/hts.h>
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+ ]], [[
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+ ]])],[
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+ AC_MSG_RESULT(yes)
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+ succeeded=yes
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+ found_system=yes
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+ ],[
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+ ])
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+ AC_LANG_POP([C++])
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+
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+ dnl if we found no hts with system layout we search for hts libraries
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+ dnl built and installed without the --layout=system option or for a staged(not installed) version
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+ if test "x$succeeded" != "xyes"; then
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+ _version=0
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+ if test "$ac_hts_path" != ""; then
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+ if test -d "$ac_hts_path" && test -r "$ac_hts_path"; then
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+ for i in `ls -d $ac_hts_path/include/hts* 2>/dev/null`; do
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+ _version_tmp=`echo $i | sed "s#$ac_hts_path##" | sed 's/\/include\/hts-//' | sed 's/_/./'`
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+ V_CHECK=`expr $_version_tmp \> $_version`
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+ if test "$V_CHECK" = "1" ; then
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+ _version=$_version_tmp
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+ fi
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+ VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
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+ HTS_CPPFLAGS="-I$ac_hts_path/include/hts-$VERSION_UNDERSCORE"
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+ done
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+ fi
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+ else
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+ for ac_hts_path in /usr /usr/local /opt /opt/local ; do
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+ if test -d "$ac_hts_path" && test -r "$ac_hts_path"; then
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+ for i in `ls -d $ac_hts_path/include/hts-* 2>/dev/null`; do
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+ _version_tmp=`echo $i | sed "s#$ac_hts_path##" | sed 's/\/include\/hts-//' | sed 's/_/./'`
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+ V_CHECK=`expr $_version_tmp \> $_version`
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+ if test "$V_CHECK" = "1" ; then
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+ _version=$_version_tmp
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+ best_path=$ac_hts_path
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+ fi
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+ done
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+ fi
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+ done
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+
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+ VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
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+ HTS_CPPFLAGS="-I$best_path/include/hts-$VERSION_UNDERSCORE"
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+ if test "$ac_hts_lib_path" = ""
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+ then
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+ HTS_LDFLAGS="-L$best_path/lib"
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+ fi
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+
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+ if test "x$HTS_ROOT" != "x"; then
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+ if test -d "$HTS_ROOT" && test -r "$HTS_ROOT" && test -d "$HTS_ROOT/stage/lib" && test -r "$HTS_ROOT/stage/lib"; then
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+ version_dir=`expr //$HTS_ROOT : '.*/\(.*\)'`
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+ stage_version=`echo $version_dir | sed 's/hts_//' | sed 's/_/./g'`
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+ stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
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+ V_CHECK=`expr $stage_version_shorten \>\= $_version`
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+ if test "$V_CHECK" = "1" -a "$ac_hts_lib_path" = "" ; then
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+ AC_MSG_NOTICE(We will use a staged hts library from $HTS_ROOT)
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+ HTS_CPPFLAGS="-I$HTS_ROOT"
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+ HTS_LDFLAGS="-L$HTS_ROOT/stage/lib"
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+ fi
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+ fi
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+ fi
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+ fi
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+
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+ CPPFLAGS="$CPPFLAGS $HTS_CPPFLAGS"
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+ export CPPFLAGS
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+ LDFLAGS="$LDFLAGS $HTS_LDFLAGS"
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+ export LDFLAGS
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+
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+ AC_LANG_PUSH(C++)
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+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
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+ @%:@include <htslib/version.hpp>
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+ ]], [[
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+ ]])],[
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+ AC_MSG_RESULT(yes)
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+ succeeded=yes
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+ found_system=yes
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+ ],[
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+ ])
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+ AC_LANG_POP([C++])
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+ fi
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+
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+ if test "$succeeded" != "yes" ; then
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+ if test "$_version" = "0" ; then
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+ AC_MSG_ERROR([[We could not detect the hts libraries (version $hts_lib_version_req_shorten or higher). If you have a staged hts library (still not installed) please specify \$HTS_ROOT in your environment and do not give a PATH to --with-hts option. If you are sure you have hts installed, then check your version number looking in <htslib/version.hpp>. See http://randspringer.de/hts for more documentation.]])
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+ else
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+ AC_MSG_NOTICE([Your hts libraries seem too old (version $_version).])
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+ fi
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+ else
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+ HTS_LIB="-lhts"
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+ AC_SUBST(HTS_CPPFLAGS)
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+ AC_SUBST(HTS_LDFLAGS)
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+ AC_SUBST(HTS_LIB)
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+ AC_DEFINE(HAVE_HTS,,[define if the HTS library is available])
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+ fi
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+
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+ CPPFLAGS="$CPPFLAGS_SAVED"
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+ LDFLAGS="$LDFLAGS_SAVED"
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+fi
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+
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+])
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diff --git a/configure.ac b/configure.ac
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index ce9936f..eba4f7a 100755
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--- a/configure.ac
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+++ b/configure.ac
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@@ -2,7 +2,7 @@ m4_include([ax_boost_base.m4])
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m4_include([ax_boost_thread.m4])
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m4_include([ax_boost_system.m4])
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m4_include([ax_boost_serialization.m4])
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-m4_include([ax_bam.m4])
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+m4_include([ax_hts.m4])
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m4_include([ax_check_zlib.m4])
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m4_include([ax_check_eigen.m4])
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@@ -33,7 +33,7 @@ AC_PROG_INSTALL
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m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
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AM_PATH_PYTHON([2.4])
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AX_BOOST_BASE([1.47.0])
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-AX_BAM
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+AX_HTS
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AX_BOOST_SYSTEM
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AX_BOOST_SERIALIZATION
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AX_BOOST_THREAD
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@@ -105,7 +105,7 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with
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CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
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CXXFLAGS="$CFLAGS"
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-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
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+CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${HTS_CPPFLAGS} ${EIGEN_CPPFLAGS}"
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user_LDFLAGS="$LDFLAGS"
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LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
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diff --git a/cufflinks.xcodeproj/project.pbxproj b/cufflinks.xcodeproj/project.pbxproj
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index ea9dce7..f021377 100644
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--- a/cufflinks.xcodeproj/project.pbxproj
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+++ b/cufflinks.xcodeproj/project.pbxproj
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@@ -748,7 +748,7 @@
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A2047A17191141C7007193FC /* libbam.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libbam.a; path = ../../../../opt/local/libIntel64/libbam.a; sourceTree = "<group>"; };
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ED1C0C7111D7D9E500CFD663 /* ax_boost_base.m4 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = ax_boost_base.m4; sourceTree = "<group>"; };
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ED1C0C7211D7D9E500CFD663 /* ax_boost_thread.m4 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = ax_boost_thread.m4; sourceTree = "<group>"; };
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- ED1C0C7411D7DA3200CFD663 /* ax_bam.m4 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = ax_bam.m4; sourceTree = "<group>"; };
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+ ED1C0C7411D7DA3200CFD663 /* ax_hts.m4 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = ax_hts.m4; sourceTree = "<group>"; };
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ED1C0CAA11D7E52400CFD663 /* ax_check_zlib.m4 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = ax_check_zlib.m4; sourceTree = "<group>"; };
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ED1C0D7911D7F94900CFD663 /* libz.dylib */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.dylib"; name = libz.dylib; path = usr/lib/libz.dylib; sourceTree = SDKROOT; };
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ED41B838127602C60000B5A2 /* cufflinks_xcode */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = cufflinks_xcode; sourceTree = BUILT_PRODUCTS_DIR; };
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diff --git a/make_bin.sh b/make_bin.sh
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index 32c2e6e..f4d3aa5 100755
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--- a/make_bin.sh
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+++ b/make_bin.sh
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@@ -2,11 +2,11 @@
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#simple script to pack up a precompiled binary package, with the boost thread
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# library statically linked in; on x86_64 Linux, libstc++ and libgcc are linked statically also
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if [[ -z "$2" ]]; then
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- echo -e "Usage:\n./make_bin.sh <package_base_name> <boost_prefix> [<bam_prefix> [<Eigen_prefix>]]"
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+ echo -e "Usage:\n./make_bin.sh <package_base_name> <boost_prefix> [<hts_prefix> [<Eigen_prefix>]]"
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exit 1
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fi
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-echo "packing up $1.tar.gz, using boost in $2, linking against $3 and using BAM in $4, using Eigen in $5"
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+echo "packing up $1.tar.gz, using boost in $2, linking against $3 and using HTS in $4, using Eigen in $5"
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mkdir $1
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#make clean
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make distclean
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@@ -38,8 +38,8 @@ fi
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# fi
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-#./configure --enable-intel64 --with-boost=$l2 --with-boost-thread=$l3 --with-bam=$l4 --with-eigen=$l5
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-./configure --with-boost=$l2 --with-boost-thread=$l2/lib/libboost_thread.a --with-boost-system=$l2/lib/libboost_system.a --with-bam=$l3 --with-eigen=$l4 --with-boost-serialization=$l2/lib/libboost_serialization.a
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+#./configure --enable-intel64 --with-boost=$l2 --with-boost-thread=$l3 --with-hts=$l4 --with-eigen=$l5
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+./configure --with-boost=$l2 --with-boost-thread=$l2/lib/libboost_thread.a --with-boost-system=$l2/lib/libboost_system.a --with-hts=$l3 --with-eigen=$l4 --with-boost-serialization=$l2/lib/libboost_serialization.a
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make
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cp src/cufflinks $1
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cp src/cuffcompare $1
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diff --git a/src/Makefile.am b/src/Makefile.am
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index b46137d..a900f19 100644
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--- a/src/Makefile.am
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+++ b/src/Makefile.am
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@@ -206,8 +206,8 @@ CLEANFILES = $(bin_SCRIPTS)
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# (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
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cufflinks_SOURCES = cufflinks.cpp
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-cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS)
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+cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS) #$(ZLIB_LDFLAGS)
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cuffcompare_SOURCES = cuffcompare.cpp
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cuffcompare_LDADD = libgc.a
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@@ -216,30 +216,30 @@ gffread_SOURCES = gffread.cpp
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gffread_LDADD = libgc.a
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cuffdiff_SOURCES = cuffdiff.cpp
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-cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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cuffquant_SOURCES = cuffquant.cpp
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-cuffquant_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-cuffquant_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+cuffquant_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+cuffquant_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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cuffnorm_SOURCES = cuffnorm.cpp
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-cuffnorm_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-cuffnorm_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+cuffnorm_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+cuffnorm_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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gtf_to_sam_SOURCES = gtf_to_sam.cpp
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-gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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#cuffcluster_SOURCES = cuffcluster.cpp
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-#cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-#cuffcluster_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+#cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+#cuffcluster_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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compress_gtf_SOURCES = compress_gtf.cpp
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-compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
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-compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
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+compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
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+compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS)
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#gtf_reads_SOURCES = gtf_reads.cpp
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-#gtf_reads_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
|
|
-#gtf_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS)
|
|
+#gtf_reads_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(HTS_LIB)
|
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+#gtf_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(HTS_LDFLAGS) #$(ZLIB_LDFLAGS)
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--
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2.33.0
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