diff options
| author | Étienne Mollier <emollier@debian.org> | 2021-11-06 19:31:45 +0100 |
|---|---|---|
| committer | Étienne Mollier <emollier@debian.org> | 2021-11-06 19:31:45 +0100 |
| commit | cbdf8676ed63cde36ac9488edd48a39737502ca8 (patch) | |
| tree | e28118032399ff458023e3a3e3380710e6b8f8f1 | |
| parent | 92f4514af4d8bfb50daf300a2fe8825c5552702a (diff) | |
| parent | a07d4c3469efc55a6e287db115112574437376b1 (diff) | |
bamtools (2.5.1+dfsg-10) unstable; urgency=medium
* Team upload.
* Add gcc11.patch (Closes: 983981)
* Remove bamtools.lintian-overrides
[dgit import unpatched bamtools 2.5.1+dfsg-10]
36 files changed, 1052 insertions, 0 deletions
diff --git a/debian/README.test b/debian/README.test new file mode 100644 index 0000000..74ce729 --- /dev/null +++ b/debian/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/debian/bamtools.1 b/debian/bamtools.1 new file mode 100644 index 0000000..593d2b2 --- /dev/null +++ b/debian/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/debian/bamtools.install b/debian/bamtools.install new file mode 100644 index 0000000..1df36c6 --- /dev/null +++ b/debian/bamtools.install @@ -0,0 +1 @@ +usr/bin/* diff --git a/debian/bamtools.manpages b/debian/bamtools.manpages new file mode 100644 index 0000000..e618c88 --- /dev/null +++ b/debian/bamtools.manpages @@ -0,0 +1 @@ +debian/bamtools.1 diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..249595c --- /dev/null +++ b/debian/changelog @@ -0,0 +1,226 @@ +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/debian/clean b/debian/clean new file mode 100644 index 0000000..991c2c6 --- /dev/null +++ b/debian/clean @@ -0,0 +1,5 @@ +bin/* +lib/* +include/* +src/toolkit/bamtools_version.h +html/ diff --git a/debian/cmake/bamtools/bamtools-config.cmake b/debian/cmake/bamtools/bamtools-config.cmake new file mode 100644 index 0000000..eb0173f --- /dev/null +++ b/debian/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/debian/control b/debian/control new file mode 100644 index 0000000..48da485 --- /dev/null +++ b/debian/control @@ -0,0 +1,111 @@ +Source: bamtools +Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> +Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>, + Andreas Tille <tille@debian.org>, + Kevin Murray <spam@kdmurray.id.au>, + Dominique Belhachemi <domibel@debian.org> +Section: science +Priority: optional +Build-Depends: debhelper-compat (= 13), + d-shlibs, + cmake, + zlib1g-dev, + libjsoncpp-dev, + help2man, + doxygen +Standards-Version: 4.5.1 +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: libbamtools2.5.1 (= ${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~) +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: libbamtools2.5.1 +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} +Breaks: libbamtools-dev (<< 2.4.0+dsfg-6) +Replaces: libbamtools-dev (<< 2.4.0+dfsg-6) +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/debian/copyright b/debian/copyright new file mode 100644 index 0000000..27c306b --- /dev/null +++ b/debian/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/debian/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..8991d38 --- /dev/null +++ b/debian/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/debian/docs b/debian/docs new file mode 100644 index 0000000..6b01fc1 --- /dev/null +++ b/debian/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/debian/libbamtools-dev.install b/debian/libbamtools-dev.install new file mode 100644 index 0000000..7687141 --- /dev/null +++ b/debian/libbamtools-dev.install @@ -0,0 +1 @@ +debian/cmake usr/share diff --git a/debian/libbamtools-doc.doc-base b/debian/libbamtools-doc.doc-base new file mode 100644 index 0000000..8c76853 --- /dev/null +++ b/debian/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/debian/libbamtools-doc.install b/debian/libbamtools-doc.install new file mode 100644 index 0000000..c49fe91 --- /dev/null +++ b/debian/libbamtools-doc.install @@ -0,0 +1 @@ +html usr/share/doc/libbamtools-dev diff --git a/debian/libbamtools.docs b/debian/libbamtools.docs new file mode 100644 index 0000000..e845566 --- /dev/null +++ b/debian/libbamtools.docs @@ -0,0 +1 @@ +README diff --git a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch new file mode 100644 index 0000000..65b0d77 --- /dev/null +++ b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch @@ -0,0 +1,42 @@ +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 + +--- + src/CMakeLists.txt | 2 +- + src/toolkit/CMakeLists.txt | 1 - + src/toolkit/bamtools_filter.cpp | 2 +- + 3 files changed, 2 insertions(+), 3 deletions(-) + +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -6,7 +6,7 @@ + # ========================== + + add_subdirectory( api ) +-add_subdirectory( third_party ) ++#add_subdirectory( third_party ) + add_subdirectory( toolkit ) + add_subdirectory( utils ) + +--- a/src/toolkit/CMakeLists.txt ++++ b/src/toolkit/CMakeLists.txt +@@ -8,7 +8,6 @@ + # set include path + include_directories( ${BamTools_SOURCE_DIR}/src/api + ${BamTools_SOURCE_DIR}/src/utils +- ${BamTools_SOURCE_DIR}/src/third_party + ) + + # compile main bamtools application +--- a/src/toolkit/bamtools_filter.cpp ++++ b/src/toolkit/bamtools_filter.cpp +@@ -16,7 +16,7 @@ + #include <utils/bamtools_utilities.h> + using namespace BamTools; + +-#include <json/json.h> ++#include <jsoncpp/json/json.h> + using namespace Json; + + #include <cstdio> diff --git a/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch new file mode 100644 index 0000000..684ea0f --- /dev/null +++ b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch @@ -0,0 +1,104 @@ +From: Dominique Belhachemi <domibel@debian.org> +Date: Fri, 19 Oct 2012 11:35:52 -0400 +Subject: remove custom ExportHeader function, use install instead + +--- + src/CMakeLists.txt | 5 +---- + src/ExportHeader.cmake | 27 --------------------------- + src/api/CMakeLists.txt | 42 +++++++++++++++++++----------------------- + src/toolkit/CMakeLists.txt | 3 +++ + 4 files changed, 23 insertions(+), 54 deletions(-) + delete mode 100644 src/ExportHeader.cmake + +--- a/src/api/CMakeLists.txt ++++ b/src/api/CMakeLists.txt +@@ -51,27 +51,23 @@ install( TARGETS BamTools + LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" + RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ) + +-# export API headers +-include(../ExportHeader.cmake) +-set(ApiIncludeDir "api") +-ExportHeader(APIHeaders api_global.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamAlgorithms.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamAlignment.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamAux.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamConstants.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamIndex.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamMultiReader.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamReader.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders BamWriter.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders IBamIODevice.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamConstants.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamHeader.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamProgram.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamProgramChain.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamReadGroup.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamReadGroupDictionary.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamSequence.h ${ApiIncludeDir}) +-ExportHeader(APIHeaders SamSequenceDictionary.h ${ApiIncludeDir}) ++install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamAlignment.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamAux.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamConstants.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamIndex.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamMultiReader.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamReader.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES BamWriter.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES IBamIODevice.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamConstants.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamHeader.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamProgram.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamProgramChain.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamReadGroup.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamReadGroupDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamSequence.h DESTINATION "include/bamtools/api" COMPONENT Development ) ++install( FILES SamSequenceDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development ) + +-set( AlgorithmsIncludeDir "api/algorithms" ) +-ExportHeader( AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir} ) ++install( FILES algorithms/Sort.h DESTINATION "include/bamtools/api/algorithms" COMPONENT Development ) +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -11,9 +11,7 @@ add_subdirectory( toolkit ) + add_subdirectory( utils ) + + # export shared headers +-include( ExportHeader.cmake ) +-set( SharedIncludeDir "shared" ) +-ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} ) ++install( FILES shared/bamtools_global.h DESTINATION "include/bamtools/shared" COMPONENT Development ) + + # configure and install pkg-config file + configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc @ONLY ) +--- a/src/ExportHeader.cmake ++++ b/src/ExportHeader.cmake +@@ -1,27 +0,0 @@ +-# +-# ExportHeader +-# +- +-function( ExportHeader MODULE FILE DEST ) +- +- # if haven't defined our custom 'build target' +- # not exactly a build target, but lets this command get +- # checked any time build step happens +- if( NOT TARGET ${MODULE} ) +- add_custom_target( ${MODULE} ALL COMMENT "Exporting ${MODULE}" ) +- endif( NOT TARGET ${MODULE} ) +- +- # get the filename (without path) +- get_filename_component( FILENAME "${FILE}" NAME ) +- +- # copy header to destination +- add_custom_command( TARGET ${MODULE} COMMAND +- ${CMAKE_COMMAND} -E copy_if_different +- "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" +- "${CMAKE_CURRENT_BINARY_DIR}/include/${DEST}/${FILENAME}" ) +- +- # make sure files are properly 'installed' +- install( FILES "${FILE}" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/bamtools/${DEST}" ) +- +-endfunction( ExportHeader ) +- diff --git a/debian/patches/0006-Doxygen-reproducibility b/debian/patches/0006-Doxygen-reproducibility new file mode 100644 index 0000000..9122f19 --- /dev/null +++ b/debian/patches/0006-Doxygen-reproducibility @@ -0,0 +1,19 @@ +From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> +Date: Thu, 24 Sep 2015 17:25:24 +1000 +Subject: Doxygen-reproducibility + +--- + docs/Doxyfile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +--- a/docs/Doxyfile ++++ b/docs/Doxyfile +@@ -853,7 +853,7 @@ HTML_STYLESHEET = + # page will contain the date and time when the page was generated. Setting + # this to NO can help when comparing the output of multiple runs. + +-HTML_TIMESTAMP = YES ++HTML_TIMESTAMP = NO + + # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, + # files or namespaces will be aligned in HTML using tables. If set to diff --git a/debian/patches/0008_Cmake_Test.patch b/debian/patches/0008_Cmake_Test.patch new file mode 100644 index 0000000..77620df --- /dev/null +++ b/debian/patches/0008_Cmake_Test.patch @@ -0,0 +1,27 @@ +Description: run simple test after compilation + The test suite can be extended once we add some small and simple bam files. +Author: Dominique Belhachemi <domibel@debian.org> + +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -15,6 +15,8 @@ cmake_policy( SET CMP0048 NEW ) + # set project name and version + project( BamTools LANGUAGES CXX VERSION 2.5.1 ) + ++enable_testing() ++ + # on macOS, MACOSX_RPATH is enabled by default on more recent versions + # of CMake. Disable this behaviour, and let user enable it if need be. + cmake_policy( SET CMP0042 OLD ) +@@ -97,3 +99,11 @@ include_directories( src ) + + # list subdirectories to build in + add_subdirectory( src ) ++ ++add_test(NAME bamtools_help ++ COMMAND bin/bamtools --help ++) ++ ++add_test(NAME bamtools_stats ++ COMMAND bin/bamtools stats -in ${CMAKE_BINARY_DIR}/../debian/sam_spec_example.bam ++) diff --git a/debian/patches/doxygen-tweak b/debian/patches/doxygen-tweak new file mode 100644 index 0000000..b02f152 --- /dev/null +++ b/debian/patches/doxygen-tweak @@ -0,0 +1,37 @@ +From: Michael R. Crusoe <crusoe@ucdavis.edu> +Subject: fixes a couple Doxygen warnings +Forwarded: https://github.com/pezmaster31/bamtools/pull/120 + +--- a/src/api/BamAlignment.h ++++ b/src/api/BamAlignment.h +@@ -149,12 +149,13 @@ private: + bool IsValidSize(const std::string& tag, const std::string& type) const; + void SetErrorString(const std::string& where, const std::string& what) const; + bool SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) const; +- ++ //! \internal + // internal data + private: + struct BamAlignmentSupportData + { + ++ //! \internal + // data members + std::string AllCharData; + uint32_t BlockLength; +@@ -163,6 +164,7 @@ private: + uint32_t QuerySequenceLength; + bool HasCoreOnly; + ++ //! \internal + // constructor + BamAlignmentSupportData() + : BlockLength(0) +@@ -177,7 +179,6 @@ private: + friend class Internal::BamWriterPrivate; + + mutable std::string ErrorString; // mutable to allow updates even in logically const methods +- //! \endinternal + }; + + // --------------------------------------------------------- diff --git a/debian/patches/gcc11.patch b/debian/patches/gcc11.patch new file mode 100644 index 0000000..2ea9d13 --- /dev/null +++ b/debian/patches/gcc11.patch @@ -0,0 +1,56 @@ +Description: force comparison operator() const, fixing ftbfs with gcc-11 +Author: Étienne Mollier <emollier@debian.org> +Bug-Debian: https://bugs.debian.org/983981 +Forwarded: not-needed +Last-Update: 2021-11-06 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bamtools.orig/src/api/internal/bam/BamMultiMerger_p.h ++++ bamtools/src/api/internal/bam/BamMultiMerger_p.h +@@ -62,7 +62,7 @@ + : m_comp(comp) + {} + +- bool operator()(const MergeItem& lhs, const MergeItem& rhs) ++ bool operator()(const MergeItem& lhs, const MergeItem& rhs) const + { + const BamAlignment& l = *lhs.Alignment; + const BamAlignment& r = *rhs.Alignment; +--- bamtools.orig/src/api/algorithms/Sort.h ++++ bamtools/src/api/algorithms/Sort.h +@@ -89,7 +89,7 @@ + {} + + // comparison function +- bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) ++ bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const + { + return sort_helper(m_order, lhs.Name, rhs.Name); + } +@@ -130,7 +130,7 @@ + {} + + // comparison function +- bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) ++ bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const + { + + // force unmapped aligmnents to end +@@ -182,7 +182,7 @@ + {} + + // comparison function +- bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) ++ bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const + { + + // force alignments without tag to end +@@ -222,7 +222,7 @@ + { + + // comparison function +- inline bool operator()(const BamTools::BamAlignment&, const BamTools::BamAlignment&) ++ inline bool operator()(const BamTools::BamAlignment&, const BamTools::BamAlignment&) const + { + return false; // returning false tends to retain insertion order + } diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..88c96ba --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,9 @@ +doxygen-tweak +0001-ignore-thirdparty-and-fix-jsoncpp.patch +0003-remove-custom-ExportHeader-function-use-install-inst.patch +0006-Doxygen-reproducibility +0008_Cmake_Test.patch +spelling +tiddit.patch +shared_and_static.patch +gcc11.patch diff --git a/debian/patches/shared_and_static.patch b/debian/patches/shared_and_static.patch new file mode 100644 index 0000000..9bf01ac --- /dev/null +++ b/debian/patches/shared_and_static.patch @@ -0,0 +1,32 @@ +Description: Build additional static lib +Author: Andreas Tille <tille@debian.org> +Last-Update: Wed, 27 May 2020 09:59:29 +0200 + +--- a/src/api/CMakeLists.txt ++++ b/src/api/CMakeLists.txt +@@ -38,18 +38,24 @@ if( WIN32 ) + endif() + + # create main BamTools API library +-add_library( BamTools ${BamToolsAPISources} ) ++add_library( BamTools SHARED ${BamToolsAPISources} ) ++add_library( BamTools_static STATIC ${BamToolsAPISources} ) + # The SONAME is bumped on every version increment + # as Bamtools does not yet guarantee a stable ABI + set_target_properties( BamTools PROPERTIES + SOVERSION "${BamTools_VERSION}" + OUTPUT_NAME "bamtools" ) ++set_target_properties( BamTools_static PROPERTIES ++ OUTPUT_NAME "bamtools" ) + target_include_directories( BamTools PRIVATE "${ZLIB_INCLUDE_DIRS}" ) + target_link_libraries( BamTools PRIVATE "${ZLIB_LIBRARIES}" "${WIN32_LIBRARIES}" ) + install( TARGETS BamTools + ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" + LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" + RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ) ++install( TARGETS BamTools_static ++ ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" ++ LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" ) + + install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development ) + install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development ) diff --git a/debian/patches/spelling b/debian/patches/spelling new file mode 100644 index 0000000..8fc861c --- /dev/null +++ b/debian/patches/spelling @@ -0,0 +1,15 @@ +From: Michael R. Crusoe <crusoe@ucdavis.edu> +Subject: Fix typo +Forwarded: https://github.com/pezmaster31/bamtools/pull/122 + +--- a/src/toolkit/bamtools_resolve.cpp ++++ b/src/toolkit/bamtools_resolve.cpp +@@ -928,7 +928,7 @@ bool ResolveTool::ResolveToolPrivate::Ch + // make sure required stats file supplied + if (!m_settings->HasStatsFile) + errors.push_back( +- "Ouptut stats filename required for -makeStats mode. Please specify one using " ++ "Output stats filename required for -makeStats mode. Please specify one using " + "-stats option."); + + // check for UseStats options diff --git a/debian/patches/tiddit.patch b/debian/patches/tiddit.patch new file mode 100644 index 0000000..ca694e6 --- /dev/null +++ b/debian/patches/tiddit.patch @@ -0,0 +1,41 @@ +Description: Add IsSupplementaryAlignment() patch from bamtools code copy + shipped with tiddit +Author: Andreas Tille <tille@debian.org> +Last-Update: Wed, 27 May 2020 09:59:29 +0200 + +--- a/src/api/BamAlignment.h ++++ b/src/api/BamAlignment.h +@@ -53,6 +53,7 @@ public: + const; // returns true if alignment is part of read that satisfied paired-end resolution + bool IsReverseStrand() const; // returns true if alignment mapped to reverse strand + bool IsSecondMate() const; // returns true if alignment is second mate on read ++ bool IsSupplementaryAlignment(void) const; // Additional patch by tiddit package + + // manipulate alignment flags + public: +--- a/src/api/BamConstants.h ++++ b/src/api/BamConstants.h +@@ -43,6 +43,7 @@ const int BAM_ALIGNMENT_READ_2 = 0x0080; + const int BAM_ALIGNMENT_SECONDARY = 0x0100; + const int BAM_ALIGNMENT_QC_FAILED = 0x0200; + const int BAM_ALIGNMENT_DUPLICATE = 0x0400; ++const int SUPPLEMENTARY = 0x0800; // Additional patch by tiddit package + + // CIGAR constants + const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X"; +--- a/src/api/BamAlignment.cpp ++++ b/src/api/BamAlignment.cpp +@@ -822,6 +822,13 @@ bool BamAlignment::IsSecondMate() const + return ((AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0); + } + ++/*! \fn bool BamAlignment::IsSupplementaryAlignment() const ++ \return \c true if ailgnment is supplementary (This is an additional patch by tiddit package) ++ */ ++bool BamAlignment::IsSupplementaryAlignment(void) const { ++ return ( (AlignmentFlag & Constants::SUPPLEMENTARY) != 0 ); ++} ++ + /*! \fn bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const + \internal + diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..c1ceeba --- /dev/null +++ b/debian/rules @@ -0,0 +1,43 @@ +#!/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,$(DEB_BUILD_OPTIONS))) + cd obj-* && ln -s src/toolkit/ bin + dh_auto_test --arch +endif + +override_dh_auto_build-indep: + doxygen -u docs/Doxyfile + doxygen docs/Doxyfile + mv docs/Doxyfile.bak docs/Doxyfile + +override_dh_auto_install-indep: + +override_dh_install-arch: + dh_install --arch + d-shlibmove --commit \ + --multiarch \ + --devunversioned \ + --exclude-la \ + --movedev debian/tmp/usr/include/* usr/include \ + --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(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/debian/salsa-ci.yml b/debian/salsa-ci.yml new file mode 100644 index 0000000..33c3a64 --- /dev/null +++ b/debian/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/debian/sam_spec_example.bam b/debian/sam_spec_example.bam Binary files differnew file mode 100644 index 0000000..7e460a1 --- /dev/null +++ b/debian/sam_spec_example.bam diff --git a/debian/sam_spec_example.sam b/debian/sam_spec_example.sam new file mode 100644 index 0000000..01490f5 --- /dev/null +++ b/debian/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/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/source/include-binaries b/debian/source/include-binaries new file mode 100644 index 0000000..130b83c --- /dev/null +++ b/debian/source/include-binaries @@ -0,0 +1 @@ +debian/sam_spec_example.bam diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..d2aa55a --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr diff --git a/debian/tests/filter_script b/debian/tests/filter_script new file mode 100644 index 0000000..e30f78c --- /dev/null +++ b/debian/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/debian/tests/run-unit-test b/debian/tests/run-unit-test new file mode 100644 index 0000000..ba0c242 --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,49 @@ +#!/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/${pkg}/filter_script . +gunzip -r * + +bamtools convert -format fastq -in sam_spec_example.bam -out test.fastq + +bamtools convert -format json -in sam_spec_example.bam -out test.json + +bamtools count -in sam_spec_example.bam + +bamtools coverage -in sam_spec_example.bam -out out + +# This test fails on ppc64el for whatever reason and is for the moment (see bug #933505) +ARCH=$(dpkg --print-architecture) +if [ "$ARCH" != "ppc64el" -a "$ARCH" != "arm64" -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/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..d9e0894 --- /dev/null +++ b/debian/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/debian/watch b/debian/watch new file mode 100644 index 0000000..4ba1cf9 --- /dev/null +++ b/debian/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 |