[med-svn] [ea-utils] 01/01: Adapt patches to new upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository ea-utils.

commit 93a7b4c5cefdce603901e2bc53905d7af9d02e7b
Author: Andreas Tille <tille at debian.org>
Date:   Mon May 8 19:31:45 2017 +0200

    Adapt patches to new upstream version
---
 debian/patches/hardening.patch           | 33 ++++++++++++--------------------
 debian/patches/makefile.patch            | 12 ++++++------
 debian/patches/name-space-conflict.patch |  4 ++--
 debian/rules                             |  2 +-
 4 files changed, 21 insertions(+), 30 deletions(-)

diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index bd42682..bb53d99 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,27 +2,18 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Sat, 25 Jul 2015 07:51:46 +0200
 Description: Propagate hardening options
 
---- a/Makefile
-+++ b/Makefile
-@@ -64,21 +64,21 @@ $(PKG).${VER}-${REL}.tar.gz: $(PKG).tar.
+--- a/clipper/Makefile
++++ b/clipper/Makefile
+@@ -66,7 +66,7 @@ $(PKG).${VER}-${REL}.tar.gz: $(PKG).tar.
  	cp $< $@
  
- %: %.c fastq-lib.cpp fastq-lib.h 
--	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
-+	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)
+ %: %.cpp fastq-lib.cpp fastq-lib.h sparsehash
+-	$(CC) $(CFLAGS) $< fastq-lib.cpp -o $@
++	$(CC) $(CFLAGS) $< fastq-lib.cpp -o $@ $(LDFLAGS)
  
- %: %.cpp fastq-lib.cpp fastq-lib.h
--	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
-+	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)
- 
- 
- %: %.c gcModel.c gcModel.h
--	$(CC) $(CFLAGS) gcModel.c -o $@ $<
-+	$(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS)
- 
- %: %.cpp gcModel.c gcModel.h
--	$(CC) $(CFLAGS) gcModel.c -o $@ $<
-+	$(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS)
+ sparsehash: sparsehash-2.0.2
+ 	cd sparsehash-2.0.2; ./configure; make
+@@ -75,7 +75,7 @@ sparsehash: sparsehash-2.0.2
  
  # why the libbam.a doesn't work?  not sure... *.o works
  sam-stats: sam-stats.cpp fastq-lib.h
@@ -39,9 +30,9 @@ Description: Propagate hardening options
 +	$(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS)
  endif
  
- fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c
--	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $<
-+	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS)
+ fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.cpp sparsehash
+-	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $<
++	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $< $(LDFLAGS)
  
  bam-filter:  bam-filter.cpp 
 -	$(CC) $(CFLAGS) fastq-lib.cpp -o $@  $< -lbamtools 
diff --git a/debian/patches/makefile.patch b/debian/patches/makefile.patch
index abce167..bf934f7 100644
--- a/debian/patches/makefile.patch
+++ b/debian/patches/makefile.patch
@@ -2,13 +2,13 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
 Last-Update: Tue, 19 Aug 2014 16:19:00 +0100
 Description: Adapt Makefile to use Debian packaged libraries
 
---- a/Makefile
-+++ b/Makefile
-@@ -77,12 +77,8 @@
- 	$(CC) $(CFLAGS) gcModel.c -o $@ $<
+--- a/clipper/Makefile
++++ b/clipper/Makefile
+@@ -74,12 +74,8 @@ sparsehash: sparsehash-2.0.2
+ 	cp -r sparsehash-2.0.2/src/sparsehash/* sparsehash/
  
  # why the libbam.a doesn't work?  not sure... *.o works
--sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h
+-sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h sparsehash
 -ifeq ($(OS),Windows_NT)
 -	$(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
 -else
@@ -19,7 +19,7 @@ Description: Adapt Makefile to use Debian packaged libraries
  
  samtools/libbam.a: samtools/*.c samtools/*.h
  	cd samtools && make libbam.a
-@@ -102,4 +98,3 @@
+@@ -102,4 +98,3 @@ bam-filter:  bam-filter.cpp
  
  clean:
  	rm -f *.o $(BIN)
diff --git a/debian/patches/name-space-conflict.patch b/debian/patches/name-space-conflict.patch
index 68af57f..42b5105 100644
--- a/debian/patches/name-space-conflict.patch
+++ b/debian/patches/name-space-conflict.patch
@@ -3,8 +3,8 @@ Last-Update: Thu, 03 Dec 2015 15:15:42 +0100
 Bug-Debian: https://bugs.debian.org/794334
 Description: Make sure the renamed binary will be called
 
---- a/randomFQ
-+++ b/randomFQ
+--- a/clipper/randomFQ
++++ b/clipper/randomFQ
 @@ -84,7 +84,7 @@ if ($mate) {
  	}
  }
diff --git a/debian/rules b/debian/rules
index 4b30abf..81808ee 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,7 +10,7 @@ export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) -I/usr/include/google
 DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 
 %:
-	dh $@
+	dh $@ --sourcedirectory=clipper
 
 override_dh_auto_install:
 	dh_auto_install -- PREFIX='$${DESTDIR}/usr'

-- 
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