debian/0000755000000000000000000000000012162331426007166 5ustar debian/control0000644000000000000000000000301512162331034010563 0ustar Source: maqview Maintainer: Debian-Med Packaging Team Uploaders: Andreas Tille , Charles Plessy Section: science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, automake, freeglut3-dev, dh-autoreconf, libxi-dev Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maqview/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/maqview/trunk/ Homepage: http://maq.sourceforge.net/maqview.shtml Package: maqview Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: graphical read alignment viewer for short gene sequences Maqview is graphical read alignment viewer. It is specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. Maqview is nothing fancy as Consed or GAP, but just a simple viewer for you to see what happens in a particular region. . In comparison to tgap-maq, the text-based read alignment viewer writen by James Bonfield, Maqview is faster and takes up much less memory and disk space in indexing. This is possibly because tgap aims to be a general-purpose viewer but Maqview fully makes use of the fact that a Maq alignment file has already been sorted. Maqview is also efficient in viewing and provides a command-line tool to quickly retrieve any region in an Maq alignment file. debian/maqview.lintian-overrides0000644000000000000000000000063611746612176014237 0ustar # maqview uses internal header files of an old copy of zlib # the API has changed in the Debian packaged version and thus we # can not simply use the Debian packaged version # upstream is contacted about this problem maqview: embedded-library usr/bin/maqindex: zlib maqview: embedded-library usr/bin/maqindex_socks: zlib maqview: embedded-library usr/bin/maqview: zlib maqview: embedded-library usr/bin/zrio: zlib debian/README.source0000644000000000000000000000175411472421544011360 0ustar Remarks to the debian source of maqview --------------------------------------- The upstream source of maqview contains a copy of an older zlib version than it is packaged for Debian. Moreover the copy of the code is wronly used in contrast to the explicite hint in the header files which say /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ it uses those header files internally. So the attempt to provide a clean source without zlib was stopped. Upstream was contacted about this problem and perhaps there is some chance to fix the source code. Meanwhile the original upstream tarball is provided with exception of the .svn dir which was contained. The .svn dir was removed and the version of the source tarball was appended by "~zlibcopy" to explicitely hint about this problem. -- Andreas Tille Wed, 16 Jul 2008 12:01:33 +0200 debian/rules0000755000000000000000000000076311746514127010264 0ustar #!/usr/bin/make -f # debian/rules file for maqview # (C) Andreas Tille # GPL %: dh $@ --with autoreconf override_dh_autoreconf: dh_autoreconf --as-needed make -f Makefile.generic maqview.1 ### The *.class files in the source package can be reproduced by simply running # javac MaqDataClient.java ### however, it is unclear whether this code is used at all override_dh_auto_clean: [ ! -f Makefile ] || $(MAKE) distclean dh_auto_clean rm -f *.1 get-orig-source: . debian/get-orig-source debian/manpages0000644000000000000000000000000411471705374010707 0ustar *.1 debian/watch0000644000000000000000000000013211764322704010221 0ustar version=3 http://sf.net/maq/maqview-([\d\.]+)\.tar\.gz \ debian debian/get-orig-source debian/upstream0000644000000000000000000000062411746516146010766 0ustar Reference: author: Li, Heng and Ruan, Jue and Durbin, Richard title: Mapping short DNA sequencing reads and calling variants using mapping quality scores journal: Genome Research volume: 18 number: 11 pages: 1851-1858 doi: 10.1101/gr.078212.108 PMID: 18714091 year: 2008 URL: http://genome.cshlp.org/content/18/11/1851.abstract eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html debian/copyright0000644000000000000000000001076011746515354011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: MaqView Upstream-Contact: Jue Ruan , Heng Li , Mengyao Zhao Source: http://sourceforge.net/projects/maq/files/ Files: * Copyright: 2007-2008, Jue Ruan License: GPL-2 Files: adler32.c crc32.c infback.c inffast.* inflate.* inftrees.* Copyright: © 1995-2005 Mark Adler License: ZIP Files: compress.c deflate.* gzio.c trees.c uncompr.c zconf.c zutil.* Copyright: © 1995-2005 Jean-loup Gailly License: ZIP Files: zlib.h: Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler License: ZIP Files: kstream.h Copyright: © 2008, Attractive Chaos License: MIT Files: stdhash.* Copyright: © 2006, Heng Li License: LGPL-2.1 Comment: Copy of code in maq package Files: debian/* Copyright: © 2010, Andreas Tille License: LGPL-2.1 License: GPL-2 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. License: LGPL-2.1 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU Lesser General Public License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. License: MIT The MIT License . 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. License: ZIP This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. debian/source/0000755000000000000000000000000011540142644010467 5ustar debian/source/format0000644000000000000000000000001411334002506011666 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000263211764323374012144 0ustar #!/bin/sh # script to download and repack source package of maqview # It was intended to remove a copy of zlib which is not # a simple straightforeward because of use of internal features # Thus this script simply removes the .svn dir for the moment PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`uscan --verbose --force-download | \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi mkdir -p ../tarballs cd ../tarballs UTAR="${PKG}-${VERSION}.tar.gz" mv ../${UTAR} . tar -xzf ${UTAR} cd $PKG # It is not possible to simply remove the zlib code because it was used # the wrong way using internal implementation features which are changed # in current zlib in Debian # rm -rf zutil.[ch] zlib.h zconf.h uncompr.c trees.[ch] inftrees.[ch] inflate.[ch] inffixed.h inffast.[ch] infback.c gzio.c deflate.[ch] crc32.[ch] compress.c adler32.c # remove useless SVN dir rm -rf .svn cd .. mv ${PKG} ${PKG}-${VERSION} GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${PKG}-${VERSION}" rm -rf "${PKG}-${VERSION}" debian/README.Debian0000644000000000000000000000110011472420772011225 0ustar maqview for Debian ------------------ The Perl files MaqIndex.pm and maqindex_socket.pl which are part of the source distribution are not installed in the binary package because there is no sign that these are actually used and there is no documentation which gives some hint about these files. Just drop the package maintainer a note if the files are needed. The same holds true for the Java MaqDataClient.java file which is in the source package as well as the result of "javac MaqDataClient.java". -- Andreas Tille Wed, 16 Jul 2008 12:01:33 +0200 debian/changelog0000644000000000000000000000415712162331304011042 0ustar maqview (0.2.5-6) unstable; urgency=low * debian/patches/fix-gcc-4.5.patch: Prevent from trying to link libglut statically. Closes: #713473 * debian/control: cme fix dpkg-control -- Andreas Tille Tue, 25 Jun 2013 17:04:23 +0200 maqview (0.2.5-5) unstable; urgency=low * debian/patches/fix-gcc-4.5.patch: Append -Xi to linker libraries Closes: #707426 * debian/control: - Add libxi6 to Build-Depends - Standard-Version: 3.9.4 (no changes needed) - removed DM-Upload-Allowed -- Andreas Tille Fri, 10 May 2013 11:42:33 +0200 maqview (0.2.5-4) unstable; urgency=low * debian/watch: call debian/get-orig-source * debian/get-orig-source: Enable download directly from uscan * debian/patches/fix-hurd-build.patch: Enable building under GNU/Hurd (Thanks to Cyril Roelandt for the patch) Closes: #675622 -- Andreas Tille Fri, 08 Jun 2012 09:13:46 +0200 maqview (0.2.5-3) unstable; urgency=low * debian/use-dpkg-buildflags.patch: Use build flags from environment to enable hardening (Thanks to Simon Ruderich for the patch) -- Andreas Tille Wed, 02 May 2012 09:42:34 +0200 maqview (0.2.5-2) unstable; urgency=low * debian/patches/gcc-4.7.patch: Enable building with g++-4.7 Closes: #667271 * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Removed quilt from Build-Depends because it is not needed * debian/rules: Use autoreconf which is more simple and transparent than the manual way to build twice in a row * debian/copyright: DEP5 (verified using `cme fix dpkg-copyright`) * debian/upstream: Reference * debhelper 9 (control+compat) - however hardening flags do not seem to propagate * debian/maqview.lintian-overrides: Different output format from lintian -- Andreas Tille Fri, 27 Apr 2012 14:44:13 +0200 maqview (0.2.5-1) unstable; urgency=low * Initial release Closes: #604497 -- Andreas Tille Mon, 22 Nov 2010 09:16:00 +0100 debian/patches/0000755000000000000000000000000012162331005010606 5ustar debian/patches/gcc-4.7.patch0000644000000000000000000000321711746512213012705 0ustar Author: Andreas Tille Date: Wed, 25 Apr 2012 14:20:16 +0200 Bug-Closed: http://bugs.debian.org/667270 Description: Build with g++ version 4.7 Just followed the hint of g++ itself which said: note: use 'this->direct_insert_aux' instead . Remark: This patch is identicall to the one applied in the source of the maq package (because the file is identical there) --- maqview-0.2.5.orig/stdhash.hh +++ maqview-0.2.5/stdhash.hh @@ -412,7 +412,7 @@ inline bool insert(const keytype_t &key) { __lh3_hash_base_class::rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 @@ -493,7 +493,7 @@ inline bool insert(const keytype_t &key, const valtype_t &val) { rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); vals[i] = val; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } @@ -503,7 +503,7 @@ inline bool insert(const keytype_t &key, valtype_t **q) { rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); *q = vals + i; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } debian/patches/fix-gcc-4.5.patch0000644000000000000000000000121612162331005013453 0ustar Author: Andreas Tille Description: Enable building with gcc-4.5 and higher LastChanged: Tue, 25 Jun 2013 17:04:23 +0200 --- a/configure.ac +++ b/configure.ac @@ -33,8 +33,8 @@ case "${host_os}" in AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], [is_static=1]) case $is_static in - 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; - 0) GLLIBS="-lGL -lglut -lm";; + 1) GLLIBS="-Wl,-Bdynamic -lGL -lGLU -lglut -lm -lX11 -lXi";; + 0) GLLIBS="-lGL -lGLU -lglut -lm -lX11 -lXi";; esac AC_SUBST([GLLIBS]);; # *) AC_MSG_ERROR([OS is not supported]);; debian/patches/fix-hurd-build.patch0000644000000000000000000000102211764324027014462 0ustar Description: Enable build under GNU/Hurd Author: Cyril Roelandt Last-Update: Sat, 2 Jun 2012 15:21:02 UTC Bug-Closed: http://bugs.debian.org/675622 --- maqview-0.2.5.orig/configure.ac +++ maqview-0.2.5/configure.ac @@ -24,7 +24,7 @@ darwin*) GLLIBS="-framework OpenGL -framework GLUT" AC_CHECK_HEADER(GLUT/glut.h, [isgl=1], [isgl=0]);; - linux*) + linux*|gnu*) AC_CHECK_HEADER(GL/glut.h, [isgl=1], [isgl=0]) case "${host_cpu}" in i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; debian/patches/use-dpkg-buildflags.patch0000644000000000000000000000520412143224501015462 0ustar Description: Use build flags from environment (dpkg-buildflags). Description: Enable propagating hardening flags and finding multiarch libraries Author: Simon Ruderich Last-Update: 10 May 2013 11:42:33 +0200 Index: maqview-0.2.5/configure.ac =================================================================== --- maqview-0.2.5.orig/configure.ac 2012-04-28 20:43:32.741129412 +0200 +++ maqview-0.2.5/configure.ac 2012-04-28 20:43:32.761129412 +0200 @@ -13,13 +13,13 @@ NONE);; *) is_static=1 AC_MSG_WARN([Library libglut will be statically linked.]) - LDFLAGS="-L${prefix}/lib" - CPPFLAGS="-I${prefix}/include";; + LDFLAGS="$LDFLAGS -L${prefix}/lib" + CPPFLAGS="$CPPFLAGS -I${prefix}/include";; esac # set CFLAGS and LDFLAGS -true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" +true_CFLAGS="$CFLAGS -g -O2 -Wall -W -DMAQ_LONGREADS" case "${host_os}" in darwin*) GLLIBS="-framework OpenGL -framework GLUT" Index: maqview-0.2.5/Makefile.generic =================================================================== --- maqview-0.2.5.orig/Makefile.generic 2012-04-28 20:43:04.181129286 +0200 +++ maqview-0.2.5/Makefile.generic 2012-04-28 20:43:32.761129412 +0200 @@ -1,7 +1,7 @@ CC= gcc CXX= g++ -CFLAGS= -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DHAVE_FREEGLUT# -pg -fprofile-arcs -ftest-coverage -CXXFLAGS= $(CFLAGS) +CFLAGS+= -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DHAVE_FREEGLUT# -pg -fprofile-arcs -ftest-coverage +CXXFLAGS:= $(CFLAGS) DFLAGS= ZOBJS= adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o \ infback.o inftrees.o trees.o uncompr.o zutil.o @@ -18,20 +18,20 @@ .SUFFIXES:.c .o .cc .c.o: - $(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@ + $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $< -o $@ .cc.o: - $(CXX) -c $(CXXFLAGS) $(DFLAGS) $< -o $@ + $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(DFLAGS) $< -o $@ all:$(PROGS) zrio:$(ZOBJS) zrio_main.o - $(CC) $(CFLAGS) -o $@ -DMAIN_ZRIO zrio_main.o zrio.o $(ZOBJS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ -DMAIN_ZRIO zrio_main.o zrio.o $(ZOBJS) maqindex:$(ZOBJS) $(OBJS) maqmap_index_main.o - $(CXX) $(CFLAGS) -o $@ $(ZOBJS) $(OBJS) maqmap_index_main.o + $(CXX) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(ZOBJS) $(OBJS) maqmap_index_main.o maqview:$(ZOBJS) $(OBJS) view_goto.o MainFrame.o view_panel.o gl_gui.o - $(CXX) $(CFLAGS) -o $@ $(ZOBJS) $(OBJS) view_goto.o view_panel.o gl_gui.o MainFrame.o $(GLLIBS) + $(CXX) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(ZOBJS) $(OBJS) view_goto.o view_panel.o gl_gui.o MainFrame.o $(GLLIBS) maqview.1:maqview.pod pod2man --center "Bioinformatics Tools" --release "maqview-$(VERSION)" maqview.pod > $@ debian/patches/series0000644000000000000000000000011711764323703012037 0ustar fix-gcc-4.5.patch gcc-4.7.patch use-dpkg-buildflags.patch fix-hurd-build.patch debian/mail_from_author0000644000000000000000000000465611516021030012440 0ustar Date: Tue, 23 Nov 2010 10:20:46 -0500 From: Heng Li To: Andreas Tille Cc: Jue Ruan , Debian Med Project List Subject: Re: Usage of zlib in MaqView Hello Andreas, Many thanks for considering to port maqview to Debian Med. Unfortunately, I am afraid that for maqview we have to include those private zlib headers because maqview must use very low-level zlib structs and functions in order to achieve random access in a generic gzip file. At the same time, although maqview still has a few features that even the most modern viewers are missing, it is not the best any more (for example, IGV, which has been ported to Debian Med, is more generic and better). If you have difficulty in porting maqview, you may consider not to include maqview in Debian Med. This would be unfortunate for us, but we are unable to drop the dependency. I am sorry. Best wishes, Heng On Nov 19, 2010, at 6:06 PM, Andreas Tille wrote: > Hello, > > I'm writing you on behalf of the Debian Med project that has the goal to > provide medical and bioinformatical software to all Debian users. I hope > you like the attempt to include MaqView into Debian amongst other packages > as they are listed here > > http://debian-med.alioth.debian.org/tasks/bio > > Because I had a request to package MaqView and have started inspecting > the code. When doing so I noticed that you are using inside zrio.h the > header files > > #include "zutil.h" > #include "inftrees.h" > #include "inflate.h" > > according to the top remark in these files > > this file should *not* be used by applications. It is > part of the implementation of the compression library and is > subject to change. Applications should only use zlib.h. > > this is not the purpose of these files. I'm asking because in Debian > the packaged zlib library should be used with applications. This is for > consistency and security reasons. > > My question is: Could you imagine to find a solution which properly uses > only zlib.h as it was intended by the zlib authors for future releases > of MaqView? > > Kind regards > > Andreas. > > -- > http://fam-tille.de -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. debian/compat0000644000000000000000000000000211746516307010376 0ustar 9 debian/docs0000644000000000000000000000001411471707043010040 0ustar NEWS README