debian/changelog

-bamtools (2.5.1+dfsg-4) UNRELEASED; urgency=medium
+bamtools (2.5.1+dfsg-4) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Trim trailing whitespace.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 13:08:22 +0000
+  [ Andreas Tille ]
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Drop useless get-orig-source target
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Trim trailing whitespace.
+  * Set upstream metadata fields: Repository.
+  * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 10 Oct 2019 12:59:38 +0200
 
 bamtools (2.5.1+dfsg-3) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -6,14 +6,14 @@ Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
            Dominique Belhachemi <domibel@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11),
-               d-shlibs (>= 0.56),
+Build-Depends: debhelper-compat (= 12),
+               d-shlibs,
                cmake,
                zlib1g-dev,
                libjsoncpp-dev,
                help2man,
                doxygen
-Standards-Version: 4.1.3
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/bamtools
 Vcs-Git: https://salsa.debian.org/med-team/bamtools.git
 Homepage: https://github.com/pezmaster31/bamtools/wiki
@@ -57,9 +57,9 @@ Multi-Arch: same
 Section: libdevel
 Depends: libbamtools2.5.1 (= ${binary:Version}),
          ${misc:Depends}
+Suggests: libbamtools-doc (= ${binary:Version})
 Breaks: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
 Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
-Suggests: libbamtools-doc (= ${binary:Version})
 Description: C++ API for manipulating BAM (genome alignment) files
  BamTools facilitates research analysis and data management using BAM
  files.  It copes with the enormous amount of data produced by current

debian/patches/fix_soversion.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 13 Jan 2017 10:09:04 +0100
-Description:  Upstream has not fully understood the concept of
- soversion and simply sets it same as upstream version.  This
- patch is fixing this.
- .
- FIXME: After the next version bump this should rather be set
- to major.minor number - or just an integer number.  However,
- for the moment the binary lib package is has added 2.4.0 and
- we can not revert this to 2.4 since its a lower number.
-
---- a/src/api/CMakeLists.txt
-+++ b/src/api/CMakeLists.txt
-@@ -34,7 +34,7 @@ set( BamToolsAPISources
- # create main BamTools API shared library
- add_library( BamTools SHARED ${BamToolsAPISources} )
- set_target_properties( BamTools PROPERTIES
--                       SOVERSION "2.4.1"
-+                       SOVERSION "2.4.0"
-                        OUTPUT_NAME "bamtools" )
- 
- # create main BamTools API static library

debian/patches/series

@@ -4,4 +4,3 @@ doxygen-tweak
 0006-Doxygen-reproducibility
 0008_Cmake_Test.patch
 spelling
-# fix_soversion.patch

debian/rules

@@ -17,8 +17,10 @@ override_dh_auto_configure-indep:
 override_dh_auto_test-indep:
 
 override_dh_auto_test-arch:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cd obj-* && ln -s src/toolkit/ bin
 	dh_auto_test --arch
+endif
 
 override_dh_auto_build-indep:
 	doxygen -u docs/Doxyfile
@@ -35,6 +37,3 @@ override_dh_install-indep:
 
 describe-current-version:
 	git describe --tags upstream | sed 's,^release-,,;s,-,+,;s,-,~,;'
-
-get-orig-source:
-	uscan --verbose --force-download --repack --compression xz

debian/upstream/metadata

-Name: BamTools
 Reference:
   Author: >
     Derek W. Barnett and Erik K. Garrison and Aaron R. Quinlan and
@@ -23,3 +22,4 @@ Registry:
   Entry: BamTools
 - Name: conda:bioconda
   Entry: bamtools
+Repository: https://github.com/pezmaster31/bamtools