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Bug#540453: ITP: samtools -- processing sequence alignments in SAM and BAM formats



Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

  Package name    : samtools
  Version         : 0.1.5c-1
  Upstream Author : Heng Li, Bob Handsaker, Jue Ruan, Colin Hercus.
  URL             : http://samtools.sourceforge.net/
  License         : MIT and NetBSD
  Programming Lang: C, Perl
  Description     : processing sequence alignments in SAM and BAM formats


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
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.



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


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/’;.



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