reinit the tree, so we can have metadata

3 files changed, 95 insertions, 0 deletions

diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch
new file mode 100644
index 000000000000..92b9a3ed58ac
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-ldflags.patch
@@ -0,0 +1,46 @@
+ configure.ac |   18 +++---------------
+ 1 files changed, 3 insertions(+), 15 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 90e612b..5a00d15 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -9,17 +9,10 @@ AC_PROG_INSTALL
+ AC_STDC_HEADERS
+ 
+ is_static=0
+-case ${prefix} in
+-  NONE);;
+-  *) is_static=1
+-     AC_MSG_WARN([Library libglut will be statically linked.])
+-     LDFLAGS="-L${prefix}/lib"
+-     CPPFLAGS="-I${prefix}/include";;
+-esac
+ 
+ # set CFLAGS and LDFLAGS
+ 
+-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS"
++true_CFLAGS="-DMAQ_LONGREADS"
+ case "${host_os}" in
+   darwin*)
+     GLLIBS="-framework OpenGL -framework GLUT"
+@@ -30,17 +23,12 @@ case "${host_os}" in
+ 	  i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";;
+ 	esac
+ 	AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"])
+-    AC_ARG_ENABLE(static, [  --enable-static         statically link GLUT (Linux Only)],
+-				  [is_static=1])
+-    case $is_static in
+-      1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";;
+-	  0) GLLIBS="-lGL -lglut -lm";;
+-    esac
++	GLLIBS="-lGL -lglut -lm -lGLU"
+ 	AC_SUBST([GLLIBS]);;
+ #  *) AC_MSG_ERROR([OS is not supported]);;
+ esac
+ AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1])
+-CFLAGS=$true_CFLAGS
++CFLAGS="${CFLAGS} $true_CFLAGS"
+ 
+ AC_CONFIG_FILES([Makefile])
+ AC_OUTPUT
diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch
new file mode 100644
index 000000000000..cd35273de66b
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-zlib.patch
@@ -0,0 +1,33 @@
+ Makefile.am |    6 +++---
+ zrio.c      |    2 +-
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index dad515a..9617eb7 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,8 +1,8 @@
+ bin_PROGRAMS = zrio maqindex maqview maqindex_socks
+-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \
+-		   infback.c inftrees.c trees.c uncompr.c zutil.c
+-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src)
++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c
++LIBS = -lz
+ zrio_SOURCES = zrio_main.c $(generic_src)
++zrio_LDADD = -lz
+ maqindex_SOURCES = maqmap_index_main.c $(generic_src)
+ maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \
+ 				  $(generic_src)				  
+diff --git a/zrio.c b/zrio.c
+index ffed00a..fe744df 100644
+--- a/zrio.c
++++ b/zrio.c
+@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void
+             totin += strm.avail_in;
+             totout += strm.avail_out;
+ 			tmp = strm.avail_out;
+-            ret = inflate_zr(&strm, Z_BLOCK);      /* return at end of block */
++            ret = inflate(&strm, Z_BLOCK);      /* return at end of block */
+             totin -= strm.avail_in;
+             totout -= strm.avail_out;
+ 			if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout);
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
new file mode 100644
index 000000000000..043208bb79b5
--- /dev/null
+++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
@@ -0,0 +1,16 @@
+ stdhash.hh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/stdhash.hh b/stdhash.hh
+index eaf98af..f22c5a6 100644
+--- a/stdhash.hh
++++ b/stdhash.hh
+@@ -493,7 +493,7 @@ public:
+ 	inline bool insert(const keytype_t &key, const valtype_t &val) {
+ 		rehash();
+ 		hashint_t i;
+-		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ 		vals[i] = val;
+ 		if (ret == 0) return true;
+ 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }