[med-svn] r2190 - trunk/packages/maq/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Tue Jul 8 04:28:39 UTC 2008
Author: plessy
Date: 2008-07-08 04:28:39 +0000 (Tue, 08 Jul 2008)
New Revision: 2190
Added:
trunk/packages/maq/trunk/debian/maq.doc-base
Modified:
trunk/packages/maq/trunk/debian/changelog
trunk/packages/maq/trunk/debian/compat
trunk/packages/maq/trunk/debian/control
trunk/packages/maq/trunk/debian/copyright
trunk/packages/maq/trunk/debian/docs
Log:
Registered maq.pdf, merged some previous packaging work, submitted ITP.
Modified: trunk/packages/maq/trunk/debian/changelog
===================================================================
--- trunk/packages/maq/trunk/debian/changelog 2008-07-07 21:38:41 UTC (rev 2189)
+++ trunk/packages/maq/trunk/debian/changelog 2008-07-08 04:28:39 UTC (rev 2190)
@@ -1,6 +1,6 @@
-maq (0.6.7-1) unstable; urgency=low
+maq (0.6.7-1) UNRELEASED; urgency=low
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #489836)
-- Charles Plessy <plessy at debian.org> Mon, 07 Jul 2008 23:37:51 +0900
Modified: trunk/packages/maq/trunk/debian/compat
===================================================================
--- trunk/packages/maq/trunk/debian/compat 2008-07-07 21:38:41 UTC (rev 2189)
+++ trunk/packages/maq/trunk/debian/compat 2008-07-08 04:28:39 UTC (rev 2190)
@@ -1 +1 @@
-6
+7
Modified: trunk/packages/maq/trunk/debian/control
===================================================================
--- trunk/packages/maq/trunk/debian/control 2008-07-07 21:38:41 UTC (rev 2189)
+++ trunk/packages/maq/trunk/debian/control 2008-07-08 04:28:39 UTC (rev 2190)
@@ -8,15 +8,38 @@
Build-Depends: cdbs, debhelper (>= 7), autotools-dev, gcc-multilib, g++-multilib,
lib64z1-dev, quilt
Standards-Version: 3.8.0
-Homepage: http://sourceforge.net/projects/maq/
+Homepage: http://maq.sourceforge.net/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
Package: maq
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: build mapping assemblies generated sequencing machines
- Maq is a software that builds mapping assemblies from short reads
- generated by the next-generation sequencing machines. It is particularly
- designed for Illumina-Solexa 1G Genetic Analyzer, which typically
- generates reads 25-35bp in length.
+Description: Mapping and Assembly with Quality
+ Maq builds mapping assemblies from short reads generated by the
+ next-generation sequencing machines. It is particularly designed for
+ Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to
+ handle ABI SOLiD data. Maq is previously known as mapass2.
+ .
+ With Maq you can:
+ o Fast align Illumina/SOLiD reads to the reference genome. With the
+ default options, one million pairs of reads can be mapped to the
+ human genome in about 10 CPU hours with less than 1G memory.
+ o Accurately measure the error probability of the alignment of each
+ individual read.
+ o Call the consensus genotypes, including homozygous and heterozygous
+ polymorphisms, with a Phred probabilistic quality assigned to each base.
+ o Find short indels with paired end reads.
+ o Accurately find large scale genomic deletions and translocations with
+ paired end reads.
+ o Discover potential CNVs by checking read depth.
+ o Evaluate the accuracy of raw base qualities from sequencers and help
+ to check the systematic errors.
+ .
+ However, Maq can NOT:
+ o Do de novo assembly. (Maq can only call the consensus by mapping reads
+ to a known reference.)
+ o Map shorts reads against themselves. (Maq can only find complete overlap
+ between reads.)
+ o Align capillary reads or 454 reads to the reference. (Maq cannot align
+ reads longer than 63bp.)
Modified: trunk/packages/maq/trunk/debian/copyright
===================================================================
--- trunk/packages/maq/trunk/debian/copyright 2008-07-07 21:38:41 UTC (rev 2189)
+++ trunk/packages/maq/trunk/debian/copyright 2008-07-08 04:28:39 UTC (rev 2190)
@@ -1,20 +1,16 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Charles Plessy <plessy at debian.org>,
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Upstream-Author: Heng Li <lh3 at sanger.ac.uk>
+Packaged-By: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-X-Debinized-Date: Mon, 07 Jul 2008 23:37:51 +0900.
-X-Source-Downloaded-From: http://sourceforge.net/projects/maq/
-X-Upstream-Author: 2003-2006 Heng Li <liheng at genomics.org.cn>
+Packaged-Date: Mon, 07 Jul 2008 23:37:51 +0900.
+Upstream-Source: http://downloads.sourceforge.net/maq/maq-0.6.7.tar.bz2
-Files: debian/*
-Copyright: © 2008 Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-License: Same as Maq itelf
-
Files: *
-License: GPL+
- This program is free software; you can redistribute it and/or modify
+License: GPL3+
+Copyright: © 2003-2008 Heng Li <lh3 at sanger.ac.uk>
+ 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 2 of the License, or
+ 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,
@@ -23,7 +19,29 @@
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, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
X-Comment: On Debian systems, the complete text of the GNU Public
License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: stdaln.*, stdhash.hh:
+Copyright: © 2003-2008 Heng Li <lh3 at sanger.ac.uk>
+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 Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Files: debian/*
+Copyright: © 2008 Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+License: Same as Maq itelf
+ (see above)
Modified: trunk/packages/maq/trunk/debian/docs
===================================================================
--- trunk/packages/maq/trunk/debian/docs 2008-07-07 21:38:41 UTC (rev 2189)
+++ trunk/packages/maq/trunk/debian/docs 2008-07-08 04:28:39 UTC (rev 2190)
@@ -1,2 +1,3 @@
NEWS
README
+maq.pdf
Added: trunk/packages/maq/trunk/debian/maq.doc-base
===================================================================
--- trunk/packages/maq/trunk/debian/maq.doc-base (rev 0)
+++ trunk/packages/maq/trunk/debian/maq.doc-base 2008-07-08 04:28:39 UTC (rev 2190)
@@ -0,0 +1,8 @@
+Document: maq
+Title: Maq — Mapping and Assembly with Quality
+Author: Heng Li <lh3 at sanger.ac.uk>
+Abstract: Maq manual page in PDF format
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/maq/maq.pdf.gz
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