New upstream version 2.1.3.3

Copyright (c) 2013, Tao Liu lab at UB and Xiaole Shirley Liu lab at DFCI

All rights reserved.

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:

    * Redistributions of source code must retain the above copyright

      notice, this list of conditions and the following disclaimer.

    * 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.

    * Neither the name of Tao Liu lab or Xiaole Shirley Liu lab 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 COPYRIGHT

HOLDERs AND 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.

 No newline at end of file

2019-09-19  Tao Liu  <vladimir.liu@gmail.com>

	MACS version 2.1.3.3

	* Features added

	1) Support Docker auto-deploy. PR #309

	2) Support Travis CI auto-testing, update unit-testing

	scripts, and enable subcommand testing on small datasets.

	3) Update README documents. #297 PR #306

	4) `cmbreps` supports more than 2 replicates. Merged from PR #304

	@Maarten-vd-Sande and PR #307 (our own chi-sq test code)

	5) `--d-min` option is added in `callpeak` and `predictd`, to

	exclude predictions of fragment size smaller than the given

	value. Merged from PR #267 @shouldsee.

	6) `--buffer-size` option is added in `predictd`, `filterdup`,

	`pileup` and `refinepeak` subcommands. Users can use this option

	to decrease memory usage while there are a large number of contigs

	in the data. Also, now `callpeak`, `predictd`, `filterdup`,

	`pileup` and `refinepeak` will suggest users to tweak

	`--buffer-size` while catching a MemoryError. #313 PR #314

	* Bugs fixed

	1) #265 Fixed a bug where the pseudocount hasn't been applied

	while calculating p-value score in ScoreTrack object.

	2) Fixed bdgbroadcall so that it will report those broad peaks

	without strong peak inside, a consistent behavior as `callpeak

	--broad`.

	3) Rename COPYING to LICENSE.

2018-10-17  Tao Liu  <vladimir.liu@gmail.com>

	MACS version 2.1.2

# INSTALL Guide For MACS

Time-stamp: <2018-10-17 16:18:48 Tao Liu>

Time-stamp: <2019-09-20 15:08:35 taoliu>

Please check the following instructions to complete your installation.

## Prerequisites

Python version must be equal to *2.7* to run MACS. I recommend

using the version *2.7.9*.

using the version *2.7.15*.

[Numpy](http://www.scipy.org/Download) (>=1.6) are required to run MACS v2. 

[Numpy](http://www.scipy.org/Download) (>=1.15) are required to run MACS v2. 

GCC is required to compile `.c` codes in MACS v2 package, and python

header files are needed. If you are using Mac OSX, I recommend you

install Xcode; if you are using Linux, you need to make sure

`python-dev` is installed.

[Cython](http://cython.org/) (>=0.18) is required *only if* you want to regenerate `.c`

files from `.pyx` files using `setup_w_cython.py` script.

[Cython](http://cython.org/) (>=0.25) is required to generate `.c`

files from `.pyx` files using `setup.py` script.

## Easy installation through PyPI

to install them again.  

Then under command line, type `pip install MACS2`. PyPI will

install Numpy and Scipy automatically if they are absent. 

install Numpy and Cython automatically if they are absent. 

To upgrade MACS2, type `pip install -U MACS2`. It will check

currently installed MACS2, compare the version with the one on PyPI

repository, download and install newer version while necessary.

Note, if you do not want pip to fix dependencies. For example, you

already have a workable Scipy and Numpy, and when 'pip install -U

MACS2', pip downloads newest Scipy and Numpy but unable to compile and

install them. This will fail the whole installation. You can pass

'--no-deps' option to pip and let it skip all dependencies. Type

`pip install -U --no-deps MACS2`.

## Install from source

MACS uses Python's distutils tools for source installations. To

 `$ python setup.py install --prefix /home/taoliu/`

If you want to re-generate `.c` files from `.pyx` files, you need

to install Cython first, then use `setup_w_cython.py` script to

replace `setup.py` script in the previous commands, such as::

 `$ python setup_w_cython.py install`

or:

  `$ python setup_w_cython.py install --prefix /home/taoliu/`

## Configure enviroment variables

BSD 3-Clause License

Copyright (c) 2019, Tao Liu lab at RPCCC and Xiaole Shirley Liu lab at DFCI

All rights reserved.

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 copyright holder 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 HOLDER 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.