Import bamtools_2.5.2+dfsg-3.debian.tar.xz

[dgit import tarball bamtools 2.5.2+dfsg-3 bamtools_2.5.2+dfsg-3.debian.tar.xz]

30 files changed, 869 insertions, 0 deletions

diff --git a/README.test b/README.test
new file mode 100644
index 0000000..74ce729
--- /dev/null
+++ b/README.test
@@ -0,0 +1,9 @@
+
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by executing
+
+    sh run-unit-test
+
+in order to confirm its integrity.
diff --git a/bamtools.1 b/bamtools.1
new file mode 100644
index 0000000..593d2b2
--- /dev/null
+++ b/bamtools.1
@@ -0,0 +1,54 @@
+.TH BAMTOOLS "1" "April 2014" "bamtools 2.3.0+dfsg" "User Commands"
+.SH NAME
+bamtools \- toolkit for manipulating BAM (genome alignment) files
+.SH SYNOPSIS
+.B bamtools
+[\-\-help] COMMAND [ARGS]
+.SH DESCRIPTION
+BamTools facilitates research analysis and data management using BAM
+files.  It copes with the enormous amount of data produced by current
+sequencing technologies that is typically stored in compressed, binary
+formats that are not easily handled by the text-based parsers commonly
+used in bioinformatics research.
+.SH OPTIONS
+.TP
+convert
+Converts between BAM and a number of other formats
+.TP
+count
+Prints number of alignments in BAM file(s)
+.TP
+coverage
+Prints coverage statistics from the input BAM file
+.TP
+filter
+Filters BAM file(s) by user\-specified criteria
+.TP
+header
+Prints BAM header information
+.TP
+index
+Generates index for BAM file
+.TP
+merge
+Merge multiple BAM files into single file
+.TP
+random
+Select random alignments from existing BAM file(s), intended more as a testing tool.
+.TP
+resolve
+Resolves paired\-end reads (marking the IsProperPair flag as needed)
+.TP
+revert
+Removes duplicate marks and restores original base qualities
+.TP
+sort
+Sorts the BAM file according to some criteria
+.TP
+split
+Splits a BAM file on user\-specified property, creating a new BAM output file for each value found
+.TP
+stats
+Prints some basic statistics from input BAM file(s)
+.PP
+See 'bamtools help COMMAND' for more information on a specific command.
diff --git a/bamtools.install b/bamtools.install
new file mode 100644
index 0000000..1df36c6
--- /dev/null
+++ b/bamtools.install
@@ -0,0 +1 @@
+usr/bin/*
diff --git a/bamtools.manpages b/bamtools.manpages
new file mode 100644
index 0000000..e618c88
--- /dev/null
+++ b/bamtools.manpages
@@ -0,0 +1 @@
+debian/bamtools.1
diff --git a/changelog b/changelog
new file mode 100644
index 0000000..4ff6265
--- /dev/null
+++ b/changelog
@@ -0,0 +1,259 @@
+bamtools (2.5.2+dfsg-3) unstable; urgency=medium
+
+  * Reduce number of tests also for armel
+    Closes: #992143
+
+ -- Andreas Tille <tille@debian.org>  Fri, 02 Dec 2022 13:52:00 +0100
+
+bamtools (2.5.2+dfsg-2) unstable; urgency=medium
+
+  * Do not try to move Doxyfile.bak which does not exist any more in doxygen
+    1.9.4
+    Closes: #1015861
+  * Build-Depends: pkg-config (since cmake is asking for it)
+  * Standards-Version: 4.6.1 (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Fri, 02 Sep 2022 19:53:29 +0200
+
+bamtools (2.5.2+dfsg-1) experimental; urgency=medium
+
+  [ Michael R. Crusoe ]
+  * Standards-Version: 4.6.0 (routine-update)
+  * refresh patches including reworking the shared & static library patch
+
+  [ Andreas Tille ]
+  * Remove Dominique Belhachemi from Uploaders (Thanks Dominique for all
+    your work)
+  * Remove unneeded lintian override
+
+  [ Étienne Mollier ]
+  * Remove gcc11.patch
+
+ -- Andreas Tille <tille@debian.org>  Fri, 18 Mar 2022 13:25:54 +0100
+
+bamtools (2.5.1+dfsg-10) unstable; urgency=medium
+
+  * Team upload.
+  * Add gcc11.patch (Closes: 983981)
+  * Remove bamtools.lintian-overrides
+
+ -- Étienne Mollier <emollier@debian.org>  Sat, 06 Nov 2021 19:31:45 +0100
+
+bamtools (2.5.1+dfsg-9) unstable; urgency=medium
+
+  [ Steffen Möller ]
+  * Update metadata - indent and ref to guix
+
+  [ Andreas Tille ]
+  * Extend means to prevent timeouts from amd64 also to armhf and s390x
+    Closes: #987023
+
+ -- Andreas Tille <tille@debian.org>  Thu, 15 Apr 2021 21:28:36 +0200
+
+bamtools (2.5.1+dfsg-8) unstable; urgency=medium
+
+  * Exclude test that times out on arm64
+    Closes: #953939
+  * Standards-Version: 4.5.1 (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Wed, 27 Jan 2021 08:26:37 +0100
+
+bamtools (2.5.1+dfsg-7) unstable; urgency=medium
+
+  * Override dh_auto_install-indep
+    Closes: #961777
+
+ -- Andreas Tille <tille@debian.org>  Fri, 29 May 2020 13:00:25 +0200
+
+bamtools (2.5.1+dfsg-6) unstable; urgency=medium
+
+  * Add IsSupplementaryAlignment() patch from bamtools code copy shipped
+    with tiddit
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Submit.
+  * Use d-shlibs
+  * Build additional static lib
+
+ -- Andreas Tille <tille@debian.org>  Wed, 27 May 2020 12:14:50 +0200
+
+bamtools (2.5.1+dfsg-5) unstable; urgency=medium
+
+  * Ignore one test that is known to fail on ppc64el architecture
+    Closes: #933505
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 10 Dec 2019 12:00:36 +0100
+
+bamtools (2.5.1+dfsg-4) unstable; urgency=medium
+
+  [ Jelmer Vernooij ]
+  * Trim trailing whitespace.
+
+  [ 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
+
+  * Point Vcs fields to salsa.debian.org
+  * Use Breaks+Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~) since the
+    includes were formerly in lib package
+    Closes: #894886
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Apr 2018 11:54:57 +0200
+
+bamtools (2.5.1+dfsg-2) unstable; urgency=medium
+
+  * Move /usr/includes to -dev from libbamtools2.4.0
+  * debian/control: add Multi-Arch hints and remove unneeded ${devlibs:Depends}
+  * Build the shared library.
+  * drop 0002-support-out-of-source-build patch, as this was fixed differently
+    upstream
+  * Match upstream's soname change
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 03 Apr 2018 04:18:02 -0700
+
+bamtools (2.5.1+dfsg-1) unstable; urgency=medium
+
+  [ Andreas Tille ]
+  * New upstream version
+  * cme fix dpkg-control
+  * debhelper 11
+
+  [ Michael R. Crusoe ]
+  * Make release ready with cme fix dpkg
+  * fix built in tests
+  * debian/rules: remove unused variables; drop custom library install; add
+    hardening
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 02 Apr 2018 09:47:32 -0700
+
+bamtools (2.4.1+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Nadiya Sitdykova ]
+  * add autopkgtest test-suite
+
+  [ Afif Elghraoui ]
+  * remove unused lintian overrides
+
+  [ Steffen Moeller ]
+  * debian/upstream/metadata: Added refs to bio.tools and OMICtools
+  * debian/copyright: Corrected case of upstream name
+  * debian/control: Updated policy compliance to 4.0.1
+
+ -- Nadiya Sitdykova <rovenskasa@gmail.com>  Mon, 07 Aug 2017 17:01:19 -0400
+
+bamtools (2.4.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 10
+  * cme fix dpkg-control
+  * d/watch: version=4
+  * Priority: optional
+  * soversion stays at 2.4.0 (FIXME: in future versions this should
+    be rather 2.5 without micro number)
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Jan 2017 10:47:00 +0100
+
+bamtools (2.4.0+dfsg-6) unstable; urgency=medium
+
+  * Whoops, forgot the '+dfsg' in my fix for the movement of the development
+    docs into their own -doc package. Thanks go to Andreas Beckmann
+    <anbe@debian.org> for his patience and help. (Closes: 817188)
+
+ -- Michael R. Crusoe <crusoe@ucdavis.edu>  Thu, 10 Mar 2016 01:38:21 -0800
+
+bamtools (2.4.0+dfsg-5) unstable; urgency=medium
+
+  * Fix the movement of the development docs into their own -doc package
+    (Closes: 817188)
+  * Fix another typo in upstream
+
+ -- Michael R. Crusoe <crusoe@ucdavis.edu>  Wed, 09 Mar 2016 00:58:33 -0800
+
+bamtools (2.4.0+dfsg-4) unstable; urgency=medium
+
+  * Lower priority to 'extra' due to dependency on libjsoncpp1
+  * Split out -doc package for library documentation & enable standalone -arch
+    and -indep building
+  * Fix spelling error from upstream
+  * Update Standards-Version
+  * Update my email address
+  * Fix Vcs-Git URL
+  * Quiet some Doxygen warnings
+  * Add gcc-6 compat
+  * Include ${devlibs} for -dev package
+  * Forwarded many patches upstream
+  * Remove the html docs directory during d/rules clean
+
+ -- Michael R. Crusoe <crusoe@ucdavis.edu>  Sat, 05 Mar 2016 09:07:48 -0800
+
+bamtools (2.4.0+dfsg-3) unstable; urgency=medium
+
+  * allows one to read bam files on big endian systems (Closes: #807979)
+  * added sam_spec_example.sam and sam_spec_example.bam files
+  * activated cmake testing framework abd added simple tests
+
+ -- Dominique Belhachemi <domibel@debian.org>  Sun, 20 Dec 2015 15:41:42 -0500
+
+bamtools (2.4.0+dfsg-2) unstable; urgency=medium
+
+  [ Kevin Murray ]
+  * Fix re-upload confusion
+  * Fix build of doxygen docs, add docs-base
+  * Use uscan file renaming to name upstream tarball bamtools-Vxxx.tar.gz
+  * Refresh patch queue
+
+  [ Andreas Tille]
+  * Fix linitan overides for bamtools
+
+ -- Kevin Murray <spam@kdmurray.id.au>  Thu, 24 Sep 2015 17:27:16 +1000
+
+bamtools (2.4.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Fix d/watch + get-orig-source target
+  * Adapt library package name to version number
+
+ -- Andreas Tille <tille@debian.org>  Sun, 05 Jul 2015 15:41:35 +0200
+
+bamtools (2.3.0+dfsg-3) unstable; urgency=medium
+
+  [ Michael R. Crusoe ]
+  * Make Doxygen documentation generation reproducible by eliminating
+    timestamps.
+
+  [ Andreas Tille ]
+  * Install cmake file
+  * Fix some issues in formatting of long descriptions (thanks for the patch
+    to Daniele Forsi <dforsi@gmail.com>)
+    Closes: #780437
+  * cme fix dpkg-control
+
+ -- Andreas Tille <tille@debian.org>  Mon, 18 May 2015 11:53:14 +0200
+
+bamtools (2.3.0+dfsg-2) unstable; urgency=medium
+
+  * Drop d-shlibs patch and add versioned Build-Depends for d-shlibs
+    Closes: #753210
+
+ -- Andreas Tille <tille@debian.org>  Mon, 30 Jun 2014 09:50:50 +0200
+
+bamtools (2.3.0+dfsg-1) unstable; urgency=low
+
+  * Initial release (Closes: #692498)
+
+ -- Andreas Tille <tille@debian.org>  Wed, 02 Apr 2014 13:11:47 +0200
diff --git a/clean b/clean
new file mode 100644
index 0000000..991c2c6
--- /dev/null
+++ b/clean
@@ -0,0 +1,5 @@
+bin/*
+lib/*
+include/*
+src/toolkit/bamtools_version.h
+html/
diff --git a/cmake/bamtools/bamtools-config.cmake b/cmake/bamtools/bamtools-config.cmake
new file mode 100644
index 0000000..eb0173f
--- /dev/null
+++ b/cmake/bamtools/bamtools-config.cmake
@@ -0,0 +1,40 @@
+# - Config file for the BamTools package
+#################################################
+#  Found at
+#    https://bitbucket.org/lunacab/ccdeep/raw/229ad7adb3700eec272a6cce36966b458bdaaa7a/bamtools-config.cmake
+#  Installed to /usr/share/cmake/bamtools
+#    according to the advise given in #761516 which links to the doc
+#     http://www.cmake.org/cmake/help/v2.8.12/cmake.html#command%3afind_package
+#  Andreas Tille <tille@debian.org>
+#################################################
+# It defines the following variables
+#  bamtools_FOUND - System has bamtols
+#  bamtools_INCLUDE_DIRS - include directories for BamTools
+#  bamtools_LIBRARIES    - libraries to link against
+#  bamtools_EXECUTABLE   - the bar executable
+ 
+
+include(FindPackageHandleStandardArgs)
+find_path(bamtools_INCLUDE_DIR api/BamReader.h 
+                  HINTS ENV BAMTOOLS_INC
+		  PATH_SUFFIXES bamtools
+		  )
+
+find_library(bamtools_LIBRARY NAMES bamtools
+             HINTS ${CMAKE_SYSTEM_LIB_PATH}
+             PATH_SUFFIXES bamtools
+             )
+
+get_filename_component(bamtools_LIB_DIR ${bamtools_LIBRARY}
+                       PATH)
+                       
+set(bamtools_LIBRARIES ${bamtools_LIB_DIR})
+set(bamtools_INCLUDE_DIRS ${bamtools_INCLUDE_DIR})
+get_filename_component(bamtools_REAL_LIBRARY ${bamtools_LIBRARY} REALPATH)
+get_filename_component(bamtools_LIB_FILE ${bamtools_REAL_LIBRARY} NAME)
+
+find_package_handle_standard_args(bamtools  DEFAULT_MSG
+                                  bamtools_LIBRARY bamtools_INCLUDE_DIR)
+
+mark_as_advanced(bamtools_LIBRARY bamtools_INCLUDE_DIR )
+
diff --git a/control b/control
new file mode 100644
index 0000000..1e74bd9
--- /dev/null
+++ b/control
@@ -0,0 +1,110 @@
+Source: bamtools
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe@debian.org>,
+           Andreas Tille <tille@debian.org>,
+           Kevin Murray <spam@kdmurray.id.au>,
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+               d-shlibs,
+               cmake,
+               zlib1g-dev,
+               libjsoncpp-dev,
+               help2man,
+               doxygen,
+               pkg-config
+Standards-Version: 4.6.1
+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
+Rules-Requires-Root: no
+
+Package: bamtools
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: toolkit 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
+ sequencing technologies that is typically stored in compressed, binary
+ formats that are not easily handled by the text-based parsers commonly
+ used in bioinformatics research.
+ .
+ BamTools provides both a C++ API for BAM file support as well as a
+ command-line toolkit.
+ .
+ This is the bamtools command-line toolkit.
+ .
+ Available bamtools commands:
+  convert  Converts between BAM and a number of other formats
+  count    Prints number of alignments in BAM file(s)
+  coverage Prints coverage statistics from the input BAM file
+  filter   Filters BAM file(s) by user-specified criteria
+  header   Prints BAM header information
+  index    Generates index for BAM file
+  merge    Merge multiple BAM files into single file
+  random   Select random alignments from existing BAM file(s), intended more
+           as a testing tool.
+  resolve  Resolves paired-end reads (marking the IsProperPair flag as needed)
+  revert   Removes duplicate marks and restores original base qualities
+  sort     Sorts the BAM file according to some criteria
+  split    Splits a BAM file on user-specified property, creating a new BAM
+           output file for each value found
+  stats    Prints some basic statistics from input BAM file(s)
+
+Package: libbamtools-dev
+Architecture: any
+Multi-Arch: same
+Section: libdevel
+Depends: libbamtools2.5.2 (= ${binary:Version}),
+         ${misc:Depends},
+         ${devlibs:Depends}
+Suggests: libbamtools-doc (= ${binary:Version})
+Breaks: libbamtools2.5.1
+Replaces: libbamtools2.5.1
+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
+ sequencing technologies that is typically stored in compressed, binary
+ formats that are not easily handled by the text-based parsers commonly
+ used in bioinformatics research.
+ .
+ BamTools provides both a C++ API for BAM file support as well as a
+ command-line toolkit.
+ .
+ This is the developers API package.
+
+Package: libbamtools2.5.2
+Architecture: any
+Multi-Arch: same
+Section: libs
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: dynamic library 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
+ sequencing technologies that is typically stored in compressed, binary
+ formats that are not easily handled by the text-based parsers commonly
+ used in bioinformatics research.
+ .
+ BamTools provides both a C++ API for BAM file support as well as a
+ command-line toolkit.
+ .
+ This is the runtime library.
+
+Package: libbamtools-doc
+Architecture: all
+Multi-Arch: foreign
+Section: doc
+Depends: ${misc:Depends}
+Description: docs for dynamic library 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
+ sequencing technologies that is typically stored in compressed, binary
+ formats that are not easily handled by the text-based parsers commonly
+ used in bioinformatics research.
+ .
+ BamTools provides both a C++ API for BAM file support as well as a
+ command-line toolkit.
+ .
+ This is the documentation for the library.
diff --git a/copyright b/copyright
new file mode 100644
index 0000000..27c306b
--- /dev/null
+++ b/copyright
@@ -0,0 +1,37 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BamTools
+Source: https://github.com/pezmaster31/bamtools
+Files-Excluded: src/third_party
+
+Files: *
+Copyright: 2009-2012 Derek Barnett <derekwbarnett@gmail.com>
+    2009-2010 Erik Garrison
+    2009-2010 Gabor Marth
+    2009-2010 Michael Stromberg
+License: Expat
+
+Files: debian/*
+Copyright: 2012 Michael R. Crusoe <michael.crusoe@gmail.com>
+           2014 Andreas Tille <tille@debian.org>
+           2015 Kevin Murray <spam@kdmurray.id.au>
+           2012,2015 Dominique Belhachemi <domibel@debian.org>
+License: Expat
+
+License: Expat
+ 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/createmanpages b/createmanpages
new file mode 100755
index 0000000..8991d38
--- /dev/null
+++ b/createmanpages
@@ -0,0 +1,9 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='<optional description of the program>' \
+            --version-string="$VERSION" bamtools > $MANDIR/bamtools.1
diff --git a/docs b/docs
new file mode 100644
index 0000000..6b01fc1
--- /dev/null
+++ b/docs
@@ -0,0 +1,4 @@
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/filter_script
+debian/sam_spec_example.bam
diff --git a/libbamtools-dev.install b/libbamtools-dev.install
new file mode 100644
index 0000000..7687141
--- /dev/null
+++ b/libbamtools-dev.install
@@ -0,0 +1 @@
+debian/cmake	usr/share
diff --git a/libbamtools-doc.doc-base b/libbamtools-doc.doc-base
new file mode 100644
index 0000000..8c76853
--- /dev/null
+++ b/libbamtools-doc.doc-base
@@ -0,0 +1,9 @@
+Document: libbamtools-dev
+Title: Bamtools C++ API Documentation
+Author: Derek Barnett <derekwbarnett@gmail.com>
+Abstract: The Doxygen-generated API documentation for the bamtools C++ library
+Section: Debian
+
+Format: HTML
+Index: /usr/share/doc/libbamtools-dev/html/index.html
+Files: /usr/share/doc/libbamtools-dev/html/*.html
diff --git a/libbamtools-doc.install b/libbamtools-doc.install
new file mode 100644
index 0000000..c49fe91
--- /dev/null
+++ b/libbamtools-doc.install
@@ -0,0 +1 @@
+html		usr/share/doc/libbamtools-dev
diff --git a/libbamtools.docs b/libbamtools.docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/libbamtools.docs
@@ -0,0 +1 @@
+README
diff --git a/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch b/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
new file mode 100644
index 0000000..eeb4031
--- /dev/null
+++ b/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
@@ -0,0 +1,30 @@
+From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Date: Wed, 7 Nov 2012 18:44:06 -0700
+Subject: ignore-thirdparty-and-fix-jsoncpp
+Forwarded: not-needed
+
+---
+ src/CMakeLists.txt              | 2 +-
+ src/toolkit/CMakeLists.txt      | 1 -
+ src/toolkit/bamtools_filter.cpp | 2 +-
+ 3 files changed, 2 insertions(+), 3 deletions(-)
+
+--- bamtools.orig/src/CMakeLists.txt
++++ bamtools/src/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-add_subdirectory(third_party)
++#add_subdirectory(third_party)
+ 
+ if(MSVC)
+     # We need full support for C++ exceptions
+--- bamtools.orig/src/toolkit/bamtools_filter.cpp
++++ bamtools/src/toolkit/bamtools_filter.cpp
+@@ -16,7 +16,7 @@
+ #include <utils/bamtools_utilities.h>
+ using namespace BamTools;
+ 
+-#include <json/json.h>
++#include <jsoncpp/json/json.h>
+ using namespace Json;
+ 
+ #include <cstdio>
diff --git a/patches/fix_soversion.patch b/patches/fix_soversion.patch
new file mode 100644
index 0000000..9aa8074
--- /dev/null
+++ b/patches/fix_soversion.patch
@@ -0,0 +1,17 @@
+Description: SONAME is only MAJOR.MINOR
+ Ist turned out that this patch is not really a good idea and its
+ better to stick with upstream soname
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 15 Oct 2021 15:08:32 +0200
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -120,7 +120,7 @@ add_library(
+ # as Bamtools does not yet guarantee a stable ABI
+ set_target_properties(
+     BamTools PROPERTIES
+-    SOVERSION ${BamTools_VERSION}
++    SOVERSION "${BamTools_VERSION_MAJOR}.${BamTools_VERSION_MINOR}"
+     OUTPUT_NAME bamtools
+     CXX_STANDARD 11
+     CXX_STANDARD_REQUIRED ON
diff --git a/patches/series b/patches/series
new file mode 100644
index 0000000..b318add
--- /dev/null
+++ b/patches/series
@@ -0,0 +1,3 @@
+0001-ignore-thirdparty-and-fix-jsoncpp.patch
+shared_and_static.patch
+#fix_soversion.patch
diff --git a/patches/shared_and_static.patch b/patches/shared_and_static.patch
new file mode 100644
index 0000000..678d062
--- /dev/null
+++ b/patches/shared_and_static.patch
@@ -0,0 +1,117 @@
+Description: Build additional static lib
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 27 May 2020 09:59:29 +0200
+
+--- bamtools.orig/src/CMakeLists.txt
++++ bamtools/src/CMakeLists.txt
+@@ -33,7 +33,7 @@
+ 
+ # create main BamTools API library
+ add_library(
+-    BamTools
++    BamTools SHARED
+ 
+     api/BamAlignment.cpp
+     api/BamMultiReader.cpp
+@@ -73,6 +73,48 @@
+     api/internal/sam/SamHeaderValidator_p.cpp
+     api/internal/utils/BamException_p.cpp
+ )
++add_library(
++    BamTools_static STATIC
++
++    api/BamAlignment.cpp
++    api/BamMultiReader.cpp
++    api/BamReader.cpp
++    api/BamWriter.cpp
++    api/SamHeader.cpp
++    api/SamProgram.cpp
++    api/SamProgramChain.cpp
++    api/SamReadGroup.cpp
++    api/SamReadGroupDictionary.cpp
++    api/SamSequence.cpp
++    api/SamSequenceDictionary.cpp
++    api/internal/bam/BamHeader_p.cpp
++    api/internal/bam/BamMultiReader_p.cpp
++    api/internal/bam/BamRandomAccessController_p.cpp
++    api/internal/bam/BamReader_p.cpp
++    api/internal/bam/BamWriter_p.cpp
++    api/internal/index/BamIndexFactory_p.cpp
++    api/internal/index/BamStandardIndex_p.cpp
++    api/internal/index/BamToolsIndex_p.cpp
++    api/internal/io/BamDeviceFactory_p.cpp
++    api/internal/io/BamFile_p.cpp
++    api/internal/io/BamFtp_p.cpp
++    api/internal/io/BamHttp_p.cpp
++    api/internal/io/BamPipe_p.cpp
++    api/internal/io/BgzfStream_p.cpp
++    api/internal/io/ByteArray_p.cpp
++    api/internal/io/HostAddress_p.cpp
++    api/internal/io/HostInfo_p.cpp
++    api/internal/io/HttpHeader_p.cpp
++    api/internal/io/ILocalIODevice_p.cpp
++    api/internal/io/RollingBuffer_p.cpp
++    api/internal/io/TcpSocketEngine_p.cpp
++    api/internal/io/TcpSocket_p.cpp
++    api/internal/sam/SamFormatParser_p.cpp
++    api/internal/sam/SamFormatPrinter_p.cpp
++    api/internal/sam/SamHeaderValidator_p.cpp
++    api/internal/utils/BamException_p.cpp
++)
++
+ 
+ # The SONAME is bumped on every version increment
+ # as Bamtools does not yet guarantee a stable ABI
+@@ -83,6 +125,12 @@
+     CXX_STANDARD 11
+     CXX_STANDARD_REQUIRED ON
+     CXX_EXTENSIONS OFF)
++set_target_properties(
++    BamTools_static PROPERTIES
++    OUTPUT_NAME bamtools
++    CXX_STANDARD 11
++    CXX_STANDARD_REQUIRED ON
++    CXX_EXTENSIONS OFF)
+ target_include_directories(
+     BamTools PRIVATE
+     ${ZLIB_INCLUDE_DIRS}
+@@ -91,6 +139,15 @@
+ target_link_libraries(
+     BamTools PRIVATE
+     ${ZLIB_LIBRARIES})
++target_include_directories(
++    BamTools_static PRIVATE
++    ${ZLIB_INCLUDE_DIRS}
++    ${CMAKE_CURRENT_SOURCE_DIR}
++    ${CMAKE_CURRENT_BINARY_DIR})
++target_link_libraries(
++    BamTools_static PRIVATE
++    ${ZLIB_LIBRARIES})
++
+ 
+ if(WIN32)
+     target_link_libraries(
+@@ -103,6 +160,9 @@
+     target_sources(
+         BamTools PRIVATE
+         api/internal/io/TcpSocketEngine_unix_p.cpp)
++    target_sources(
++        BamTools_static PRIVATE
++        api/internal/io/TcpSocketEngine_unix_p.cpp)
+ endif()
+ 
+ if(EnableNodeJS)
+@@ -195,6 +255,13 @@
+     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+ 
+ install(
++    TARGETS BamTools_static
++    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
++    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
++    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
++
++
++install(
+     TARGETS bamtools_cmd
+     ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+     LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
diff --git a/rules b/rules
new file mode 100755
index 0000000..61fa368
--- /dev/null
+++ b/rules
@@ -0,0 +1,42 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
+
+%:
+	dh $@
+
+override_dh_auto_test-indep:
+
+override_dh_auto_test-arch:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	cd obj-* && ln -s src/toolkit/ bin
+	dh_auto_test --arch
+endif
+
+override_dh_auto_build-indep:
+	doxygen -u docs/Doxyfile
+	doxygen docs/Doxyfile
+
+override_dh_auto_install-indep:
+
+override_dh_install-arch:
+	dh_install --arch
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --movedev debian/tmp/usr/include/* usr/include \
+		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
+		    debian/tmp/usr/lib/*/*.so
+
+override_dh_install-indep:
+	dh_install --indep
+	rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js
+	ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js
+
+describe-current-version:
+	git describe --tags upstream | sed 's,^release-,,;s,-,+,;s,-,~,;'
diff --git a/salsa-ci.yml b/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/salsa-ci.yml
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff --git a/sam_spec_example.bam b/sam_spec_example.bam
new file mode 100644
index 0000000..7e460a1
--- /dev/null
+++ b/sam_spec_example.bam
diff --git a/sam_spec_example.sam b/sam_spec_example.sam
new file mode 100644
index 0000000..01490f5
--- /dev/null
+++ b/sam_spec_example.sam
@@ -0,0 +1,8 @@
+@HD	VN:1.5	SO:coordinate
+@SQ	SN:ref	LN:45
+r001	99	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG	*
+r002	0	ref	9	30	3S6M1P1I4M	*	0	0	AAAAGATAAGGATA	*
+r003	0	ref	9	30	5S6M	*	0	0	GCCTAAGCTAA	*	SA:Z:ref,29,-,6H5M,17,0;
+r004	0	ref	16	30	6M14N5M	*	0	0	ATAGCTTCAGC	*
+r003	2064	ref	29	17	6H5M	*	0	0	TAGGC	*	SA:Z:ref,9,+,5S6M,30,1;
+r001	147	ref	37	30	9M	=	7	-39	CAGCGGCAT	*	NM:i:1
diff --git a/source/format b/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/source/include-binaries b/source/include-binaries
new file mode 100644
index 0000000..130b83c
--- /dev/null
+++ b/source/include-binaries
@@ -0,0 +1 @@
+debian/sam_spec_example.bam
diff --git a/tests/control b/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/tests/filter_script b/tests/filter_script
new file mode 100644
index 0000000..e30f78c
--- /dev/null
+++ b/tests/filter_script
@@ -0,0 +1,17 @@
+{
+  "filters" : 
+    [
+      { "id" : "inAnyErrorReadGroup",
+        "tag" : "RG:ERR*"
+      },
+      { "id" : "highMapQuality",
+        "mapQuality" : ">=75"
+      },
+      { "id" : "bothMatesMapped",
+        "isMapped" : "true",
+        "isMateMapped" : "true"
+      }
+    ],
+  "rule" : "!inAnyErrorReadGroup & (highMapQuality | bothMatesMapped)"
+}
+
diff --git a/tests/run-unit-test b/tests/run-unit-test
new file mode 100644
index 0000000..57a9fb3
--- /dev/null
+++ b/tests/run-unit-test
@@ -0,0 +1,50 @@
+#!/bin/sh -e
+
+pkg=bamtools
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
+
+cp -a /usr/share/doc/${pkg}/sam_spec_example.bam .
+cp -a /usr/share/doc/${pkg}/filter_script .
+gunzip -r *
+
+bamtools convert -format fastq -in sam_spec_example.bam -out test.fastq
+
+bamtools convert -format json -in sam_spec_example.bam -out test.json
+
+bamtools count -in sam_spec_example.bam
+
+bamtools coverage -in sam_spec_example.bam -out out
+
+# This test fails on ppc64el for whatever reason and is for the moment (see bug #933505)
+# The test is also problematic for armel (see bug #992143)
+ARCH=$(dpkg --print-architecture)
+if [ "$ARCH" != "ppc64el" -a "$ARCH" != "arm64" -a "$ARCH" != "armel"-a "$ARCH" != "armhf" -a "$ARCH" != "s390x"  ] ; then
+   bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
+else
+   if [ "$ARCH" = "ppc64el" ] ; then
+      echo "The following test is known to fail on ppc64el architecture (see bug #933505)"
+   else
+      echo "The following test is known to time out on $ARCH architecture (see bug #953939)"
+   fi
+   echo "bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam"
+fi
+
+bamtools header -in sam_spec_example.bam
+
+bamtools index -in sam_spec_example.bam
+
+bamtools random -n 100 -in sam_spec_example.bam -out out.bam
+
+bamtools revert -in sam_spec_example.bam -out out.bam
+
+bamtools sort -in sam_spec_example.bam -out out.bam
+
+bamtools split -mapped -in sam_spec_example.bam
+
+bamtools stats -in sam_spec_example.bam
diff --git a/upstream/metadata b/upstream/metadata
new file mode 100644
index 0000000..d9e0894
--- /dev/null
+++ b/upstream/metadata
@@ -0,0 +1,31 @@
+Bug-Submit: https://github.com/pezmaster31/bamtools/issues/new
+Reference:
+ - Author: >
+    Derek W. Barnett and Erik K. Garrison and Aaron R. Quinlan and
+    Michael P. Stromberg and Gabor T. Marth
+   Title: >
+    BamTools: a C++ API and toolkit for analyzing and managing BAM files
+   Journal: Bioinformatics
+   Year: 2011
+   Volume: 27
+   Number: 12
+   Pages: 1691-2
+   DOI: 10.1093/bioinformatics/btr174
+   PMID: 21493652
+   URL: http://bioinformatics.oxfordjournals.org/content/27/12/1691
+   eprint: >
+    http://bioinformatics.oxfordjournals.org/content/27/12/1691.full.pdf+html
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_11315
+ - Name: SciCrunch
+   Entry: SCR_015987
+ - Name: bio.tools
+   Entry: BamTools
+ - Name: conda:bioconda
+   Entry: bamtools
+ - Name: guix
+   Entry: bamtools
+Repository: https://github.com/pezmaster31/bamtools.git
+Bug-Database: https://github.com/pezmaster31/bamtools/issues
+Repository-Browse: https://github.com/pezmaster31/bamtools
diff --git a/watch b/watch
new file mode 100644
index 0000000..4ba1cf9
--- /dev/null
+++ b/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg.*//,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/bamtools-$1.tar.gz/" \
+https://github.com/pezmaster31/bamtools/tags .*/v?(\d[\d\.]+)\.tar\.gz