[med-svn] [crac] 02/03: Fix patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository crac.

commit 9d6f92870d8905db34e751e0b65aa3075642705d
Author: Andreas Tille <tille at debian.org>
Date:   Sun Sep 11 15:02:47 2016 +0200

    Fix patches
---
 debian/patches/use_debian_packaged_libgzstream.patch | 20 ++++++++++++++++++++
 .../patches/use_debian_packaged_libjellyfish.patch   |  2 +-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/debian/patches/use_debian_packaged_libgzstream.patch b/debian/patches/use_debian_packaged_libgzstream.patch
index 12802a0..5bcdb29 100644
--- a/debian/patches/use_debian_packaged_libgzstream.patch
+++ b/debian/patches/use_debian_packaged_libgzstream.patch
@@ -23,3 +23,23 @@ Description: Use Debian packaged libgzstream
  if INCLUDED_GKARRAYS
    SUBDIRS += libGkArrays
  endif
+@@ -131,7 +131,7 @@ crac_SOURCES =                    \
+   locateServer.cpp locateServer.h \
+   utils.cpp utils.h \
+   Bitset.cpp Bitset.h
+-crac_LDADD = @abs_builddir@/libSSA/libSSA.a @abs_builddir@/libReadsInfo/libReadsInfo.a @abs_builddir@/libgzstream/libgzstream.a @abs_builddir@/libReadsReader/libReadsReader.a 
++crac_LDADD = @abs_builddir@/libSSA/libSSA.a @abs_builddir@/libReadsInfo/libReadsInfo.a @abs_builddir@/libReadsReader/libReadsReader.a 
+ 
+ #crac_index_SOURCES = @abs_srcdir@/libSSA/cracIndex.cpp
+ #crac_index_LDADD = @abs_builddir@/libSSA/libSSA.a
+@@ -143,8 +143,8 @@ crac-emt: @abs_builddir@/libSSA/crac-emt
+ 	$(LN_S) -f $^ $@
+ 
+ 
+-AM_LDFLAGS = -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L at abs_builddir@/libSSA -L at abs_builddir@/libReadsInfo -L at abs_builddir@/libgzstream -L at abs_builddir@/libReadsReader  #-pg # for Gprof
+-AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bwt -I at abs_srcdir@/libgzstream 
++AM_LDFLAGS = -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L at abs_builddir@/libSSA -L at abs_builddir@/libReadsInfo -L at abs_builddir@/libReadsReader  #-pg # for Gprof
++AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bw
+ 
+ if INCLUDED_JELLYFISH
+   AM_LDFLAGS += -L at abs_builddir@/libJellyfish-2.0/.libs
diff --git a/debian/patches/use_debian_packaged_libjellyfish.patch b/debian/patches/use_debian_packaged_libjellyfish.patch
index 068e64a..60d45a6 100644
--- a/debian/patches/use_debian_packaged_libjellyfish.patch
+++ b/debian/patches/use_debian_packaged_libjellyfish.patch
@@ -14,7 +14,7 @@ Description: Use Debian packaged libjellyfish-2.0
  crac_SOURCES =                    \
    basic.h const.h types.h         \
 @@ -147,8 +144,8 @@ AM_LDFLAGS = -lm -lpthread -lhts -lSSA -
- AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bwt -I at abs_srcdir@/libgzstream 
+ AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bw
  
  if INCLUDED_JELLYFISH
 -  AM_LDFLAGS += -L at abs_builddir@/libJellyfish-2.0/.libs

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