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commit 1961741b0b13f066c004b06bb14033c78f70447d
Author: Andreas Tille <ti...@debian.org>
Date: Fri Jan 13 13:30:31 2017 +0100
Use debian packaged vcflib and drop own code copy
---
debian/changelog | 3 +-
debian/control | 3 +-
debian/copyright | 29 +------------
debian/patches/series | 1 +
debian/patches/use_debian_packaged_vcflib.patch | 57 +++++++++++++++++++++++++
5 files changed, 64 insertions(+), 29 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 57603f6..f937e32 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-tvc (5.0.3+dfsg-2) UNRELEASED; urgency=medium
+tvc (5.0.3+dfsg1-1) UNRELEASED; urgency=medium
* Team maintenance in Debian Med team
* cme fix dpkg-control
* debhelper 10
+ * use Debian packaged vcflib
-- Andreas Tille <ti...@debian.org> Fri, 13 Jan 2017 11:17:08 +0100
diff --git a/debian/control b/debian/control
index d2b724a..299b5b3 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,8 @@ Build-Depends: debhelper (>= 10),
libbamtools-dev,
libjsoncpp-dev,
libarmadillo-dev,
- libboost-math-dev
+ libboost-math-dev,
+ libvcflib-dev
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/tvc.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/tvc.git
diff --git a/debian/copyright b/debian/copyright
index 0863ff4..8b7ca29 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: tvc
Source: https://github.com/iontorrent
-
+Files-Excluded: external/vcflib
Files: *
Copyright: 2010-2014 Ion Torrent Systems, Inc.
@@ -44,31 +44,6 @@ License: MIT
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
-
-Files: external/vcflib/*
-Copyright: 2008-2009 Genome Research Ltd (GRL)
- 2008-2010 Broad Institute / Massachusetts Institute of Technology
- 2010-2012 Erik Garrison
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
-
Files: debian/*
Copyright: 2015 Dominique Belhachemi <domi...@debian.org>
License: GPL-2+
diff --git a/debian/patches/series b/debian/patches/series
index a7aaa65..f92360d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ bamtools.patch
help.patch
hurd.patch
sse.patch
+use_debian_packaged_vcflib.patch
diff --git a/debian/patches/use_debian_packaged_vcflib.patch
b/debian/patches/use_debian_packaged_vcflib.patch
new file mode 100644
index 0000000..0786be9
--- /dev/null
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -0,0 +1,57 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -18,10 +18,9 @@ configure_file (
+ )
+
+
+-set(ION_VCFLIB_DIR external/vcflib)
+ set(ION_FREEBAYES_DIR external/freebayes)
+
+-include_directories(${ION_VCFLIB_DIR})
++include_directories("/usr/include/vcflib")
+ include_directories(${ION_FREEBAYES_DIR}/src)
+
+ include_directories("/usr/include/jsoncpp")
+@@ -78,17 +77,6 @@ set(tvcSRCS
+ VariantCaller/EnsembleEval/StackEngine.cpp
+ VariantCaller/EnsembleEval/CrossHypotheses.cpp
+
+- # TODO: Actually build vcflib as a static library and link to variant
caller.
+- # TODO2: Resolve bgzf.c collisions between vcflib and bamtools
+- ${ION_VCFLIB_DIR}/Variant.cpp
+- ${ION_VCFLIB_DIR}/split.cpp
+- ${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
+- ${ION_VCFLIB_DIR}/tabixpp/index.c
+- ${ION_VCFLIB_DIR}/tabixpp/bgzf.c
+- ${ION_VCFLIB_DIR}/smithwaterman/LeftAlign.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp
+ ${ION_FREEBAYES_DIR}/src/AlleleParser.cpp
+
+ BaseCaller/PIDloop.cpp
+@@ -120,7 +108,7 @@ add_executable(tvcassembly
+ ${PROJECT_BINARY_DIR}/IonVersion.cpp
+ )
+
+-target_link_libraries(tvcassembly bamtools z pthread jsoncpp)
++target_link_libraries(tvcassembly bamtools z pthread jsoncpp vcflib)
+
+
+ add_executable(tvcutils
+@@ -130,15 +118,6 @@ add_executable(tvcutils
+ VariantCaller/tvcutils/unify_vcf.cpp
+ VariantCaller/TargetsManager.cpp
+ Util/OptArgs.cpp
+- ${ION_VCFLIB_DIR}/Variant.cpp
+- ${ION_VCFLIB_DIR}/split.cpp
+- ${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
+- ${ION_VCFLIB_DIR}/tabixpp/index.c
+- ${ION_VCFLIB_DIR}/tabixpp/bgzf.c
+- ${ION_VCFLIB_DIR}/smithwaterman/LeftAlign.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp
+- ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp
+ ${PROJECT_BINARY_DIR}/IonVersion.cpp
+ )
+
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