--- /dev/null
+Source: samtools
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Standards-Version: 3.8.2
+Homepage: http://samtools.sourceforge.net
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
+
+Package: samtools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the BAM format. It imports from and exports to the SAM (Sequence
+ Alignment/Map) format, does sorting, merging and indexing, and allows to
+ retrieve reads in any regions swiftly. It is designed to work on a stream, and
+ is able to open a BAM (not SAM) file on a remote FTP server.
+
+Package: libbam-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: manipulates nucleotide sequence alignments in BAM or SAM format
+ The BAM library provides I/O and various operations on manipulating nucleotide
+ sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
+ Alignment/Map) format. It now supports importing from or exporting to TAM,
+ sorting, merging, generating pileup, and quickly retrieval of reads overlapped
+ with a specified region.
--- /dev/null
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name : SAMtools
+Contact : SAMtools mailing list <samtools-help@lists.sourceforge.net>
+Source : http://downloads.sourceforge.net/sourceforge/samtools/samtools-0.1.5c.tar.bz2
+
+Copyright : © 2008–2009, Genome Research Ltd.
+License : MIT
+
+ 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.
+
+Files : bgzf.*, bgzip.c
+Copyright : © 2008 Broad Institute / Massachusetts Institute of Technology
+License : MIT
+
+The license of the above files have been confirmed upstream and their headers
+will be corrected in the next release. See:
+http://samtools.svn.sourceforge.net/viewvc/samtools?view=rev&revision=441
+
+
+Files : razf.*
+Name : RAZF : Random Access compressed(Z) File
+Copyright : 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
+License : Similar to NetBSD license.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+
+Files : misc/md5.*
+Name : MD5 Message Digest Algorithm
+Copyright : © 1990, RSA Data Security, Inc.
+License :
+
+ License to copy and use this software is granted provided that
+ it is identified as the "RSA Data Security, Inc. MD5 Message
+ Digest Algorithm" in all material mentioning or referencing this
+ software or this function.
+
+ License is also granted to make and use derivative works
+ provided that such works are identified as "derived from the RSA
+ Data Security, Inc. MD5 Message Digest Algorithm" in all
+ material mentioning or referencing the derived work.
+
+ RSA Data Security, Inc. makes no representations concerning
+ either the merchantability of this software or the suitability
+ of this software for any particular purpose. It is provided "as
+ is" without express or implied warranty of any kind.
+
+ These notices must be retained in any copies of any part of this
+ documentation and/or software.
+
+The above source files for MD5 support will be replaced in the next SAMtools
+release by the public domain implementation of ‘http://www.fourmilab.ch/md5/’.
--- /dev/null
+DOI: 10.1093/bioinformatics/btp352
+Homepage: http://samtools.sourceforge.net
+PMID: 19505943
+Reference: |
+ @article{HengLi06082009,
+ author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup, },
+ title = {{The Sequence Alignment/Map (SAM) Format and SAMtools}},
+ journal = {Bioinformatics},
+ volume = {},
+ number = {},
+ pages = {btp352},
+ doi = {10.1093/bioinformatics/btp352},
+ year = {2009},
+ URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1},
+ eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf}
+ }
+Repository: https://samtools.svn.sourceforge.net/svnroot/samtools
projects / samtools.git / commitdiff