Import pbbam_0.7.4+ds-1.debian.tar.xz

[dgit import tarball pbbam 0.7.4+ds-1 pbbam_0.7.4+ds-1.debian.tar.xz]

diff --git a/README.source b/README.source
new file mode 100644 (file)
index 0000000..c29c516
--- /dev/null
+++ b/README.source
@@ -0,0 +1,10 @@
+pbbam for Debian
+----------------
+
+* The swig bindings require a version of swig higher than 3.0.2 (currently in unstable).
+  Without this, python and R bindings cannot be built.
+
+
+
+ -- Afif Elghraoui <afif@ghraoui.name>, Sun,  6 Sep 2015 13:57:45 -0700
+

diff --git a/TODO b/TODO
new file mode 100644 (file)
index 0000000..c86d636
--- /dev/null
+++ b/TODO
@@ -0,0 +1,5 @@
+* Manpages for pbbamtools programs
+
+* package python and R bindings
+
+* package API documentation

diff --git a/changelog b/changelog
new file mode 100644 (file)
index 0000000..7fa6fb0
--- /dev/null
+++ b/changelog
@@ -0,0 +1,57 @@
+pbbam (0.7.4+ds-1) unstable; urgency=medium
+
+  * New upstream release snapshot
+    - Exclude dependency convenience copy
+    - Update patches
+    - Update running of tests at build-time
+    - Update .install files
+    - Update autopkgtest commands
+  * Use debhelper compat 10
+  * libpbbam-dev: depend on libssl-dev
+
+ -- Afif Elghraoui <afif@debian.org>  Sat, 21 Jan 2017 23:48:21 -0800
+
+pbbam (0.7.0-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.7.0
+  * Update patches
+
+ -- Afif Elghraoui <afif@debian.org>  Sun, 30 Oct 2016 14:31:49 -0700
+
+pbbam (0.5.0-3) unstable; urgency=low
+
+  * Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed.
+    Thanks to Steve Langasek (Closes: #841671)
+
+ -- Afif Elghraoui <afif@debian.org>  Sun, 23 Oct 2016 14:07:27 -0700
+
+pbbam (0.5.0-2) unstable; urgency=low
+
+  * libpbbam-dev: add dependency on libhts-dev
+
+ -- Afif Elghraoui <afif@debian.org>  Sun, 17 Jul 2016 23:29:34 -0700
+
+pbbam (0.5.0-1) unstable; urgency=medium
+
+  * New upstream revision (git 79ab246 from 2016-02-23)
+  * Declare additional copyrights to avoid repacking tarball
+  * Update patches
+  * Update Standards-Version to 3.9.8
+  * Use encrypted protocols for VCS URLs
+  * Clean up d/control and d/rules
+  * Use dh-exec for library installation rather than sed-within-d/rules
+  * Set up build-time tests for command-line tools
+  * Add binary package for command-line tools
+  * Install library to main library path
+  * Configure autopkgtests
+  * Use documentation page as Homepage
+  * Remove build-dependency on doxygen
+  * Add TODO list
+
+ -- Afif Elghraoui <afif@debian.org>  Tue, 05 Jul 2016 03:25:49 -0700
+
+pbbam (0.1.0~20150813+git4e9e417+dfsg-1) unstable; urgency=low
+
+  * Initial release (Closes: #798220)
+
+ -- Afif Elghraoui <afif@ghraoui.name>  Fri, 18 Sep 2015 02:40:24 -0700

diff --git a/compat b/compat
new file mode 100644 (file)
index 0000000..f599e28
--- /dev/null
+++ b/compat
@@ -0,0 +1 @@
+10

diff --git a/control b/control
new file mode 100644 (file)
index 0000000..94d6fbd
--- /dev/null
+++ b/control
@@ -0,0 +1,84 @@
+Source: pbbam
+Section: libs
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif@debian.org>
+Build-Depends:
+       debhelper (>= 10),
+       dh-exec,
+       cmake,
+       python,
+#      swig3.0,
+       libboost-dev (>= 1.54),
+       zlib1g-dev,
+       libssl-dev,
+       libhts-dev,
+# Test-Depends:
+#      libgtest-dev,
+       python-cram,
+       samtools,
+Standards-Version: 3.9.8
+Homepage: http://pbbam.readthedocs.org/en/latest/index.html
+Vcs-Git: https://anonscm.debian.org/git/debian-med/pbbam.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbbam.git
+
+Package: pbbamtools
+Section: science
+Architecture: any
+Depends:
+       ${shlibs:Depends},
+       ${misc:Depends},
+       libpbbam (= ${binary:Version}),
+Recommends: samtools
+Description: processing Pacific Biosciences binary alignment/map files
+ The BAM format is a binary, compressed, record-oriented container format
+ for raw or aligned sequence reads. The associated SAM format is a text
+ representation of the same data. The specifications for BAM/SAM are maintained
+ by the SAM/BAM Format Specification Working Group.
+ .
+ PacBio-produced BAM files are fully compatible with the BAM specification,
+ but makes use of the extensibility mechanisms of the BAM specification to
+ encode PacBio-specific information.
+ .
+ This package provides command-line utilities for working with PacBio BAM
+ files.
+
+Package: libpbbam
+Architecture: any
+Multi-Arch: same
+Pre-Depends:
+       ${misc:Pre-Depends}
+Depends:
+       ${shlibs:Depends},
+       ${misc:Depends},
+Description: Pacific Biosciences binary alignment/map (BAM) library
+ The BAM format is a binary, compressed, record-oriented container format
+ for raw or aligned sequence reads. The associated SAM format is a text
+ representation of the same data. The specifications for BAM/SAM are maintained
+ by the SAM/BAM Format Specification Working Group.
+ .
+ PacBio-produced BAM files are fully compatible with the BAM specification,
+ but makes use of the extensibility mechanisms of the BAM specification to
+ encode PacBio-specific information. The pbbam library provides tools to
+ work with these files
+
+Package: libpbbam-dev
+Section: libdevel
+Architecture: any
+Depends:
+       libpbbam (= ${binary:Version}),
+       libhts-dev,
+       libssl-dev,
+       ${misc:Depends},
+Description: Pacific Biosciences binary alignment/map (BAM) library (headers)
+ The BAM format is a binary, compressed, record-oriented container format
+ for raw or aligned sequence reads. The associated SAM format is a text
+ representation of the same data. The specifications for BAM/SAM are maintained
+ by the SAM/BAM Format Specification Working Group.
+ .
+ PacBio-produced BAM files are fully compatible with the BAM specification,
+ but makes use of the extensibility mechanisms of the BAM specification to
+ encode PacBio-specific information. The pbbam library provides tools to
+ work with these files
+ .
+ This package contains the library header files.

diff --git a/copyright b/copyright
new file mode 100644 (file)
index 0000000..431dafc
--- /dev/null
+++ b/copyright
@@ -0,0 +1,156 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbbam
+Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
+Source: https://github.com/PacificBiosciences/pbbam
+Files-Excluded: third-party
+
+Files: *
+Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
+License: PacBio-BSD-3-Clause
+
+Files: cmake/FindCSharp.cmake
+       cmake/FindMono.cmake
+       cmake/UseCSharp.cmake
+       cmake/UseDotNetFrameworkSdk.cmake
+       cmake/UseMono.cmake
+Copyright: 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
+Comment: These files are from GDCM (as indicated in the file headers).
+        The license terms have been retrieved from there.
+License: MM-BSD-3-Clause
+
+Files: src/pugixml/*
+Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com>
+          2003 Kristen Wegner <kristen@tima.net>
+License: MIT
+
+Files: tools/common/OptionParser.*
+Copyright: 2010 Johannes Weißl <jargon@molb.org>
+License: BSD-3-Clause or BSD-2-Clause
+
+Files: debian/*
+Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
+License: PacBio-BSD-3-Clause
+
+License: PacBio-BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted (subject to the limitations in the
+ disclaimer below) provided that the following conditions are met:
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above
+    copyright notice, this list of conditions and the following
+    disclaimer in the documentation and/or other materials provided
+    with the distribution.
+ 3. Neither the name of Pacific Biosciences nor the names of its
+    contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
+ .
+ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+ BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT  SHALL PACIFIC BIOSCIENCES OR ITS
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+License: MM-BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ 1. Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+ 3. Neither name of Mathieu Malaterre, or CREATIS, nor the names of any
+    contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to
+    endorse or promote products derived from this software without specific
+    prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the University nor the names of its contributors
+    may be used to endorse or promote products derived from this software
+    without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 
+ A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE HOLDERS OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: BSD-2-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
+ WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+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.

diff --git a/libpbbam-dev.install b/libpbbam-dev.install
new file mode 100644 (file)
index 0000000..0f2a4df
--- /dev/null
+++ b/libpbbam-dev.install
@@ -0,0 +1 @@
+include/*      usr/include

diff --git a/libpbbam.install b/libpbbam.install
new file mode 100755 (executable)
index 0000000..bc95dd6
--- /dev/null
+++ b/libpbbam.install
@@ -0,0 +1,2 @@
+#!/usr/bin/dh-exec
+*/lib/*        usr/lib/${DEB_HOST_MULTIARCH}

diff --git a/libpbbam.lintian-overrides b/libpbbam.lintian-overrides
new file mode 100644 (file)
index 0000000..5e4d24f
--- /dev/null
+++ b/libpbbam.lintian-overrides
@@ -0,0 +1,6 @@
+# Upstream has not yet stabilized the API.
+# This library is so far only used by a closely-related set of programs.
+shlib-without-versioned-soname usr/lib/x86_64-linux-gnu/libpbbam.so libpbbam.so
+# Because of the lack of versioned soname, the library itself contains
+# the libpbbam.so file, so there's no need for a symlink.
+dev-pkg-without-shlib-symlink usr/lib/x86_64-linux-gnu/libpbbam.so usr/lib/x86_64-linux-gnu/libpbbam.so

diff --git a/libpbbam.triggers b/libpbbam.triggers
new file mode 100644 (file)
index 0000000..c302335
--- /dev/null
+++ b/libpbbam.triggers
@@ -0,0 +1 @@
+activate-noawait       ldconfig

diff --git a/patches/remove-bam2sam.patch b/patches/remove-bam2sam.patch
new file mode 100644 (file)
index 0000000..a4dec35
--- /dev/null
+++ b/patches/remove-bam2sam.patch
@@ -0,0 +1,18 @@
+Description: Exclude the bam2sam utility
+ It is a convenience tool provided by upstream to avoid depending on
+ samtools. We actually have trouble building it in Debian and have
+ easy access to samtools.
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: not-needed
+Last-Update: 2016-07-04
+
+--- pbbam.orig/tools/CMakeLists.txt
++++ pbbam/tools/CMakeLists.txt
+@@ -39,7 +39,6 @@
+     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}")
+ 
+     # tools
+-    add_subdirectory(bam2sam)
+     add_subdirectory(pbindex)
+     add_subdirectory(pbindexdump)
+     add_subdirectory(pbmerge)

diff --git a/patches/series b/patches/series
new file mode 100644 (file)
index 0000000..78015f5
--- /dev/null
+++ b/patches/series
@@ -0,0 +1,2 @@
+ssl-md5.patch
+remove-bam2sam.patch

diff --git a/patches/ssl-md5.patch b/patches/ssl-md5.patch
new file mode 100644 (file)
index 0000000..9c4ce98
--- /dev/null
+++ b/patches/ssl-md5.patch
@@ -0,0 +1,24 @@
+Description: Use libssl for md5.h rather than cram
+ cram/md5.h was part of HTSlib [1] (seems to have been removed in the current
+ development tree), but those headers are not installed by that
+ package's build system. md5.h in particular has a very generic function,
+ served apparently by libssl. Furthermore, the cram/* headers are not intended
+ to be used directly [2]. This patch uses libssl to provide md5.h for this
+ package.
+ .
+ 1. https://anonscm.debian.org/cgit/debian-med/htslib.git/tree/cram/md5.h?id=12251926b9d0265738d701bb0add6fe9d070ccb3
+ 2. http://sourceforge.net/p/samtools/mailman/message/33488076/
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: no
+Last-Update: 2015-10-30
+--- pbbam.orig/src/MD5.cpp
++++ pbbam/src/MD5.cpp
+@@ -40,7 +40,7 @@
+ // Author: Brett Bowman
+ 
+ #include "pbbam/MD5.h"
+-#include <cram/md5.h>
++#include <openssl/md5.h>
+ 
+ namespace PacBio {
+ namespace BAM {

diff --git a/pbbamtools.install b/pbbamtools.install
new file mode 100644 (file)
index 0000000..7380180
--- /dev/null
+++ b/pbbamtools.install
@@ -0,0 +1 @@
+*/bin  /usr

diff --git a/rules b/rules
new file mode 100755 (executable)
index 0000000..f1eb875
--- /dev/null
+++ b/rules
@@ -0,0 +1,52 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+export LC_ALL=C.UTF-8
+include /usr/share/dpkg/default.mk
+
+DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM))
+generated_data_dir = $(CURDIR)/gendata
+
+%:
+         dh $@
+
+override_dh_auto_configure:
+       dh_auto_configure -- \
+       -DPacBioBAM_build_shared=ON \
+       -DPacBioBAM_build_tests=OFF \
+       -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \
+       -DCMAKE_SKIP_RPATH=ON \
+       -DHTSLIB_INCLUDE_DIRS=/usr/include \
+       -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \
+       -DCMAKE_SHARED_LINKER_FLAGS="$(LDFLAGS)"
+#      -DPacBioBAM_wrap_python=ON \
+#      -DPacBioBAM_wrap_r=ON
+
+override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
+       mkdir -p $(generated_data_dir)
+       python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir)
+       BINDIR=`find $$PWD -name bin -type d`; \
+       LIBDIR=`find $$PWD -name lib -type d`; \
+       PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \
+       cram -v $^
+
+override_dh_installchangelogs:
+       dh_installchangelogs CHANGELOG.md
+
+override_dh_auto_clean:
+       dh_auto_clean
+       find -name "*.deb.t" -delete
+       $(RM) -r $(generated_data_dir)
+
+%.deb.t: %.t.in
+       sed \
+       -e 's/$$BAM2SAM/samtools view/g' \
+       -e 's/\-\-header\-only/-H/g' \
+       -e 's/\-\-no\-header//g' \
+       -e 's|@PacBioBAM_BinDir@/||g' \
+       -e 's|$$TOOLS_BIN/||g' \
+       -e 's|@PacBioBAM_TestsDir@|$(CURDIR)/tests|g' \
+       -e 's|@PacBioBAM_VERSION@|$(DEB_VERSION_UPSTREAM)|g' \
+       -e 's|@GeneratedTestDataDir@|$(generated_data_dir)|g' \
+       $< > $@
+

diff --git a/source/format b/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/tests/control b/tests/control
new file mode 100644 (file)
index 0000000..98aedfd
--- /dev/null
+++ b/tests/control
@@ -0,0 +1,9 @@
+Test-Command: debian/rules override_dh_auto_test
+Depends:
+       make,
+       python,
+       pbbamtools,
+       python-cram,
+Restrictions:
+       needs-recommends,
+       rw-build-tree,

diff --git a/watch b/watch
new file mode 100644 (file)
index 0000000..d4dc1e9
--- /dev/null
+++ b/watch
@@ -0,0 +1,2 @@
+# Upstream is currently not tagging releases. The library itself does
+# not yet provide a stable interface