[Collab-qa-commits] r2246 - in packages-metadata: f m
Charles Plessy
plessy at alioth.debian.org
Sat Apr 28 03:00:29 UTC 2012
Author: plessy
Date: 2012-04-28 03:00:29 +0000 (Sat, 28 Apr 2012)
New Revision: 2246
Added:
packages-metadata/f/fastdnaml.upstream
packages-metadata/f/fastlink.upstream
packages-metadata/m/maqview.upstream
Modified:
packages-metadata/m/maqview.copyright
Log:
Daily automatic umegaya push
Added: packages-metadata/f/fastdnaml.upstream
===================================================================
--- packages-metadata/f/fastdnaml.upstream (rev 0)
+++ packages-metadata/f/fastdnaml.upstream 2012-04-28 03:00:29 UTC (rev 2246)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Gary J. Olsen and Hideo Matsuda and Ray Hagstrom and Ross Overbeek
+ Title: "fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood"
+ Journal: Comput Appl Biosci
+ Year: 1994
+ Volume: 10
+ Number: 1
+ Pages: 41-48
+ DOI: 10.1093/bioinformatics/10.1.41
+ PMID: 8193955
+ URL: http://bioinformatics.oxfordjournals.org/content/10/1/41.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/10/1/41.full.pdf+html
Added: packages-metadata/f/fastlink.upstream
===================================================================
--- packages-metadata/f/fastlink.upstream (rev 0)
+++ packages-metadata/f/fastlink.upstream 2012-04-28 03:00:29 UTC (rev 2246)
@@ -0,0 +1,11 @@
+Reference:
+ Author: R. W. Cottingham Jr. and R. M. Idury and A. A. Schaffer
+ Title: Faster Sequential Genetic Linkage Computations
+ Journal: American Journal of Human Genetics
+ Year: 1993
+ Volume: 53
+ Number: 1
+ Pages: 252-263
+ PMID: 8317490
+ URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1682239/
+ eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1682239/pdf/ajhg00052-0258.pdf
Modified: packages-metadata/m/maqview.copyright
===================================================================
--- packages-metadata/m/maqview.copyright 2012-04-27 03:00:29 UTC (rev 2245)
+++ packages-metadata/m/maqview.copyright 2012-04-28 03:00:29 UTC (rev 2246)
@@ -1,57 +1,75 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MaqView
+Upstream-Contact: Jue Ruan <ruanjue at genomics.org.cn>, Heng Li <lh3 at sanger.ac.uk>,
+ Mengyao Zhao <zhaomengyao at gmail.com>
+Source: http://sourceforge.net/projects/maq/files/
-Name : MaqView: Mapping and Assembly with Qualities
-Contact : Jue Ruan <ruanjue at genomics.org.cn>, Heng Li <lh3 at sanger.ac.uk>,
- Mengyao Zhao <zhaomengyao at gmail.com>
-Source : http://sourceforge.net/projects/maq/files/
-
-License: GPL2
+Files: *
Copyright: 2007-2008, Jue Ruan <ruanjue at genomics.org.cn>
+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 <http://www.gnu.org/licenses/>.
+Files: adler32.c crc32.c infback.c inffast.* inflate.* inftrees.*
+Copyright: © 1995-2005 Mark Adler
+License: ZIP
-On Debian systems, the complete text of the GNU General Public License version
-2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+Files: compress.c deflate.* gzio.c trees.c uncompr.c zconf.c zutil.*
+Copyright: © 1995-2005 Jean-loup Gailly
+License: ZIP
-
-Files: adler32.c, crc32.c, infback.c, inffast.[ch], inflate.[ch], inftrees.[ch]
-Copyright: © 1995-2005 Mark Adler
-Files: compress.c, deflate.[ch], gzio.c, trees.c, uncompr.c, zconf.c, zutil.[ch]
-Copyright: © 1995-2005 Jean-loup Gailly
Files: zlib.h:
Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
- 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.
+License: ZIP
- 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:
+Files: kstream.h
+Copyright: © 2008, Attractive Chaos <attractivechaos at aol.co.uk>
+License: MIT
- 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.
+Files: stdhash.*
+Copyright: © 2006, Heng Li <lh3lh3 at gmail.com>
+License: LGPL-2.1
+Comment: Copy of code in maq package
+Files: debian/*
+Copyright: © 2010, Andreas Tille <tille at debian.org>
+License: LGPL-2.1
-Files: kstream.h
-Copyright: © 2008, Attractive Chaos <attractivechaos at aol.co.uk>
-Source: http://attractivechaos.wordpress.com/programs/
-License: The MIT License
+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 <http://www.gnu.org/licenses/>.
+ .
+ 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 <http://www.gnu.org/licenses/>.
+ .
+ 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
@@ -59,10 +77,10 @@
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
@@ -72,27 +90,20 @@
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-Files: stdhash.[ch]*
-Copyright: © 2006, Heng Li <lh3lh3 at gmail.com>
-Remark: Copy of code in maq package
-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.
+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.
- 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 <http://www.gnu.org/licenses/>.
-
- 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’.
-
-Files: debian/*
-Copyright: © 2010, Andreas Tille <tille at debian.org>
-License: Same as MaqView itelf
- (see above)
Added: packages-metadata/m/maqview.upstream
===================================================================
--- packages-metadata/m/maqview.upstream (rev 0)
+++ packages-metadata/m/maqview.upstream 2012-04-28 03:00:29 UTC (rev 2246)
@@ -0,0 +1,12 @@
+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
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