Htslib
Htslib
https://github.com/samtools/htslib
generic indexer for TAB-delimited genome position files
Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosme), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name.
This version of tabix is built from the HTSlib source.
Licensing
License
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License
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Debian: Charles Plessy <plessy@debian.org>
Verified on
24 September 2014
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License: mit
License
Verified by
Debian: Charles Plessy <plessy@debian.org>
Verified on
24 September 2014
Notes
License: various_bsd-3-clause
Various_BSD-3-Clause The files in the 'cram' directory are under one or both of the following licenses.
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.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD 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 GENOME RESEARCH LTD 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.
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.
3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 COPYRIGHT OWNER 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.License
Verified by
Debian: Charles Plessy <plessy@debian.org>
Verified on
24 September 2014
Notes
License: solar-md5
solar-MD5 This is an OpenSSL-compatible implementation of the RSA Data Security, Inc. MD5 Message-Digest Algorithm (RFC 1321).
Homepage: http://openwall.info/wiki/people/solar/software/public- domain-source-code/md5
Author: Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
This software was written by Alexander Peslyak in 2001. No copyright is claimed, and the software is hereby placed in the public domain. In case this attempt to disclaim copyright and place the software in the public domain is deemed null and void, then the software is Copyright (c) 2001 Alexander Peslyak and it is hereby released to the general public under the following terms:
Redistribution and use in source and binary forms, with or without modification, are permitted.
There's ABSOLUTELY NO WARRANTY, express or implied.
Leaders and contributors
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Debian (Ref) | https://tracker.debian.org/pkg/htslib | |
| Download | https://github.com/samtools/htslib/archive/1.1.tar.gz |
Software prerequisites
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.
The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.