[med-svn] r12914 - in trunk/packages/genometools/trunk/debian: . patches

[Sascha Steinbiss]

Author: sascha-guest
Date: 2013-02-05 18:13:50 +0000 (Tue, 05 Feb 2013)
New Revision: 12914

Modified:
   trunk/packages/genometools/trunk/debian/changelog
   trunk/packages/genometools/trunk/debian/patches/adding_soname
   trunk/packages/genometools/trunk/debian/patches/libbam-fix
Log:
New upstream release 1.5.0


Modified: trunk/packages/genometools/trunk/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog	2013-02-05 09:23:24 UTC (rev 12913)
+++ trunk/packages/genometools/trunk/debian/changelog	2013-02-05 18:13:50 UTC (rev 12914)
@@ -1,3 +1,23 @@
+genometools (1.5.0-1) unstable; urgency=low
+
+  * New upstream release
+  * bugfixes and cleanups
+  * development tool `gt sain' added to run an induced suffix array sorting 
+    algorithm
+  * the -typecheck option in the `gt gff3` and `gt gff3validator` tools 
+    now also validates parent (part-of) relationships, see -help output for 
+    details
+  * new option -encseq besides -seqfile(s) and -regionmapping to select a
+    encseq index as a sequence source
+  * GtBioseq backend switched to GtEncseq
+  * GtSeqCol is now an interface, GtEncseqCol added
+  * GtRankedList added
+  * GtSNPAnnotatorStream and `gt snpper' tool added
+  * node sorting code is now aware of MD5 hash presence
+  * compatibility with old Pango versions inproved
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>  Tue, 05 Feb 2013 18:52:22 +0100
+
 genometools (1.4.2-4) unstable; urgency=low
 
   * Remove shlibs.local file 

Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/adding_soname	2013-02-05 09:23:24 UTC (rev 12913)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname	2013-02-05 18:13:50 UTC (rev 12914)
@@ -1,6 +1,6 @@
 --- a/Makefile
 +++ b/Makefile
-@@ -86,6 +86,7 @@
+@@ -96,6 +96,7 @@
    SHARED_OBJ_NAME_EXT:=.so
    SHARED:=-shared
  endif
@@ -8,7 +8,7 @@
  
  # compiled executables
  GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
-@@ -238,7 +239,7 @@
+@@ -249,7 +250,7 @@
  
  # add necessary shared lib dependencies then not building them ourselves
  ifeq ($(useshared),yes)
@@ -17,7 +17,7 @@
             -llua5.1-filesystem -llua5.1-des56 -lbam
  else
    DEPLIBS:=
-@@ -517,7 +518,7 @@
+@@ -532,7 +533,7 @@
  
  ifdef DESTDIR
    prefix:=$(DESTDIR)$(prefix)
@@ -26,7 +26,7 @@
  
  # allow to set patch program
  patch ?= patch
-@@ -595,8 +596,9 @@
+@@ -610,8 +611,9 @@
                                            $(ADDITIONAL_ZLIBS)
  	@echo "[link $(@F)]"
  	@test -d $(@D) || mkdir -p $(@D)
@@ -38,7 +38,7 @@
  
  lib/libtecla.a: $(LIBTECLA_OBJ)
  	@echo "[link $(@F)]"
-@@ -934,7 +936,8 @@
+@@ -950,7 +952,8 @@
  ifdef RANLIB
  	$(RANLIB) $(prefix)/lib/libgenometools.a
  endif

Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/libbam-fix	2013-02-05 09:23:24 UTC (rev 12913)
+++ trunk/packages/genometools/trunk/debian/patches/libbam-fix	2013-02-05 18:13:50 UTC (rev 12914)
@@ -1,6 +1,6 @@
 --- a/Makefile
 +++ b/Makefile
-@@ -240,7 +240,7 @@
+@@ -251,7 +251,7 @@
  # add necessary shared lib dependencies then not building them ourselves
  ifeq ($(useshared),yes)
    DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
@@ -9,7 +9,7 @@
  else
    DEPLIBS:=
  endif
-@@ -576,6 +576,10 @@
+@@ -591,6 +591,10 @@
  	@$(RANLIB) $@
  endif
  
@@ -20,7 +20,7 @@
  lib/libgenometools.a: obj/gt_config.h  $(LIBGENOMETOOLS_OBJ)
  	@echo "[link $(@F)]"
  	@test -d $(@D) || mkdir -p $(@D)
-@@ -593,12 +597,13 @@
+@@ -608,12 +612,13 @@
  lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
                                            $(LIBGENOMETOOLS_OBJ) \
                                            $(ADDITIONAL_SO_DEPS) \
@@ -36,7 +36,7 @@
  
  lib/libtecla.a: $(LIBTECLA_OBJ)
  	@echo "[link $(@F)]"
-@@ -619,51 +624,61 @@
+@@ -634,51 +639,61 @@
  
  $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \
                                               lib/libgenometools.a \