New upstream version 2.29.0+dfsg

test/multicov/two_blocks.bam.bai

test/genomecov/two_blocks.bam

test/shift/genome.len

test/split/exp

src/utils/htslib/test/test-bcf-translate

src/utils/htslib/test/test_realn

test/*/exp

test/*/obs

test/genomecov/pair-chip.bam

test/bigchroms/bigx.fasta

test/bigchroms/bigx.fasta.fai

		    GNU GENERAL PUBLIC LICENSE

		       Version 2, June 1991

 Copyright (C) 1989, 1991 Free Software Foundation, Inc.,

 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

 Everyone is permitted to copy and distribute verbatim copies

 of this license document, but changing it is not allowed.

			    Preamble

  The licenses for most software are designed to take away your

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		    GNU GENERAL PUBLIC LICENSE

   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

  0. This License applies to any program or other work which contains

a notice placed by the copyright holder saying it may be distributed

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is covered only if its contents constitute a work based on the

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Whether that is true depends on what the Program does.

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	    How to Apply These Terms to Your New Programs

  If you develop a new program, and you want it to be of the greatest

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free software which everyone can redistribute and change under these terms.

  To do so, attach the following notices to the program.  It is safest

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the "copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>

    Copyright (C) <year>  <name of author>

    This program is free software; you can redistribute it and/or modify

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    (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

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    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.,

    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Also add information on how to contact you by electronic and paper mail.

If the program is interactive, make it output a short notice like this

when it starts in an interactive mode:

    Gnomovision version 69, Copyright (C) year name of author

    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.

    This is free software, and you are welcome to redistribute it

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The hypothetical commands `show w' and `show c' should show the appropriate

parts of the General Public License.  Of course, the commands you use may

be called something other than `show w' and `show c'; they could even be

mouse-clicks or menu items--whatever suits your program.

You should also get your employer (if you work as a programmer) or your

school, if any, to sign a "copyright disclaimer" for the program, if

necessary.  Here is a sample; alter the names:

  Yoyodyne, Inc., hereby disclaims all copyright interest in the program

  `Gnomovision' (which makes passes at compilers) written by James Hacker.

  <signature of Ty Coon>, 1 April 1989

  Ty Coon, President of Vice

This General Public License does not permit incorporating your program into

proprietary programs.  If your program is a subroutine library, you may

consider it more useful to permit linking proprietary applications with the

library.  If this is what you want to do, use the GNU Lesser General

Public License instead of this License.

The MIT License

Copyright (c) 2009-2019     Aaron Quinlan

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

First created through urgency and adrenaline by Aaron Quinlan Spring 2009. 

Maintained by the Quinlan Laboratory at the University of Virginia.

1. **Lead developers**:           Aaron Quinlan, Neil Kindlon

1. **Lead developers**:           Aaron Quinlan, Hao Hoou, Brent Pedersen, Neil Kindlon

2. **Significant contributions**: Assaf Gordon, Royden Clark, John Marshall, Brent Pedersen, Ryan Dale

3. **Repository**:                https://github.com/arq5x/bedtools2

4. **Stable releases**:           https://github.com/arq5x/bedtools2/releases

5. **Documentation**:             http://bedtools.readthedocs.org

6. **License**:                   Released under GNU public license version 2 (GPL v2).

6. **License**:                   Released under MIT license

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