New upstream version 2.1.2.1

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

	MACS version 2.1.2

	* New features

	1) Added missing BEDPE support. And enable the support for BAMPE

	and BEDPE formats in 'pileup', 'filterdup' and 'randsample'

	subcommands. When format is BAMPE or BEDPE, The 'pileup' command

	will pile up the whole fragment defined by mapping locations of

	the left end and right end of each read pair. Thank @purcaro

	2) Added options to callpeak command for tweaking max-gap and

	min-len during peak calling. Thank @jsh58!

	3) The callpeak option "--to-large" option is replaced with

	"--scale-to large".

	4) The randsample option "-t" has been replaced with "-i".

	* Bug fixes

	1) Fixed memory issue related to #122 and #146

	2) Fixed a bug caused by a typo. Related to #249, Thank @shengqh

	3) Fixed a bug while setting commandline qvalue cutoff.

	4) Better describe the 5th column of narrowPeak. Thank @alexbarrera

	5) Fixed the calculation of average fragment length for paired-end

	data. Thank @jsh58

	6) Fixed bugs caused by khash while computing p/q-value and log

	likelihood ratios. Thank @jsh58

	7) More spelling tweaks in source code. Thank @mr-c

2016-03-09  Tao Liu  <vladimir.liu@gmail.com>

	MACS version 2.1.1 20160309

======================

INSTALL Guide For MACS

======================

Time-stamp: <2014-06-17 15:27:24 Tao Liu>

# INSTALL Guide For MACS

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

Please check the following instructions to complete your installation.

Prerequisites

=============

## Prerequisites

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

using the version *2.7.2*.

using the version *2.7.9*.

Numpy_ (>=1.6) are required to run MACS v2. 

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

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

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.

`python-dev` is installed.

Cython_ (>=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/) (>=0.18) is required *only if* you want to regenerate `.c`

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

.. _Numpy: http://www.scipy.org/Download

.. _Cython: http://cython.org/

Easy installation through PyPI

==============================

## Easy installation through PyPI

The easiest way to install MACS2 is through PyPI system. Get pip_ if

it's not available in your system. *Note* if you have already

installed numpy and scipy system-wide, you can use ```virtualenv

--system-site-packages``` to let your virtual Python environment have

installed numpy and scipy system-wide, you can use `virtualenv

--system-site-packages` to let your virtual Python environment have

access to system-wide numpy and scipy libraries so that you don't need

to install them again.  

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

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

install Numpy and Scipy automatically if they are absent. 

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

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.

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```.

.. _pip: http://www.pip-installer.org/en/latest/installing.html

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

Install from source

===================

## Install from source

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

install a source distribution of MACS, unpack the distribution tarball

and open up a command terminal. Go to the directory where you unpacked

MACS, and simply run the install script::

MACS, and simply run the install script:

 $ python setup.py install

 `$ python setup.py install`

By default, the script will install python library and executable

codes globally, which means you need to be root or administrator of

administrator of that machine if you want their help. If you need to

provide a nonstandard install prefix, or any other nonstandard

options, you can provide many command line options to the install

script. Use the –help option to see a brief list of available options::

script. Use the –help option to see a brief list of available options:

 $ python setup.py --help

 `$ python setup.py --help`

For example, if I want to install everything under my own HOME

directory, use this command::

directory, use this command:

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

 `$ 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::

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

 `$ python setup_w_cython.py install`

or::

or:

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

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

Configure enviroment variables

==============================

## Configure enviroment variables

After running the setup script, you might need to add the install

location to your ``PYTHONPATH`` and ``PATH`` environment variables. The

location to your `PYTHONPATH` and `PATH` environment variables. The

process for doing this varies on each platform, but the general

concept is the same across platforms.

PYTHONPATH

~~~~~~~~~~

### PYTHONPATH

To set up your ``PYTHONPATH`` environment variable, you'll need to add the

value ``PREFIX/lib/pythonX.Y/site-packages`` to your existing

``PYTHONPATH``. In this value, X.Y stands for the major–minor version of

To set up your `PYTHONPATH` environment variable, you'll need to add the

value `PREFIX/lib/pythonX.Y/site-packages` to your existing

`PYTHONPATH`. In this value, X.Y stands for the major–minor version of

Python you are using (such as 2.7 ; you can find this with

``sys.version[:3]`` from a Python command line). ``PREFIX`` is the install

`sys.version[:3]` from a Python command line). `PREFIX` is the install

prefix where you installed MACS. If you did not specify a prefix on

the command line, MACS will be installed using Python's sys.prefix

value.

On Linux, using bash, I include the new value in my ``PYTHONPATH`` by

adding this line to my ``~/.bashrc``::

On Linux, using bash, I include the new value in my `PYTHONPATH` by

adding this line to my `~/.bashrc`::

 $ export PYTHONPATH=/home/taoliu/lib/python2.7/site-packages:$PYTHONPATH

 `$ export PYTHONPATH=/home/taoliu/lib/python2.7/site-packages:$PYTHONPATH`

Using Windows, you need to open up the system properties dialog, and

locate the tab labeled Environment. Add your value to the ``PYTHONPATH``

variable, or create a new ``PYTHONPATH`` variable if there isn't one

locate the tab labeled Environment. Add your value to the `PYTHONPATH`

variable, or create a new `PYTHONPATH` variable if there isn't one

already.

PATH

~~~~

### PATH

Just like your ``PYTHONPATH``, you'll also need to add a new value to your

Just like your `PYTHONPATH`, you'll also need to add a new value to your

PATH environment variable so that you can use the MACS command line

directly. Unlike the ``PYTHONPATH`` value, however, this time you'll need

to add ``PREFIX/bin`` to your PATH environment variable. The process for

updating this is the same as described above for the ``PYTHONPATH``

directly. Unlike the `PYTHONPATH` value, however, this time you'll need

to add `PREFIX/bin` to your PATH environment variable. The process for

updating this is the same as described above for the `PYTHONPATH`

variable::

 $ export PATH=/home/taoliu/bin:$PATH

 `$ export PATH=/home/taoliu/bin:$PATH`

--

Tao Liu <vladimir.liu@gmail.com>

COPYING

ChangeLog

INSTALL.rst

INSTALL.md

MANIFEST.in

README.rst

README.md

setup.py

setup_w_cython.py

MACS2/Constants.py

MACS2/PeakModel.pyx

MACS2/Pileup.c

MACS2/Pileup.pyx

MACS2/Poisson.c

MACS2/PosVal.pyx

MACS2/Prob.c

MACS2/Prob.pyx

MACS2/Signal.c

MACS2/IO/PairedEndTrack.c

MACS2/IO/PairedEndTrack.pyx

MACS2/IO/Parser.c

MACS2/IO/Parser.h

MACS2/IO/Parser.pyx

MACS2/IO/PeakIO.c

MACS2/IO/PeakIO.pyx

MACS2/IO/ScoreTrack.c

MACS2/IO/ScoreTrack.pyx

MACS2/IO/__init__.py

MACS2/IO/test_processing.py

MACS2/IO/test_threading.py

MACS2/data/__init__.py

MACS2/data/g0.01.dat

MACS2/data/g0.05.dat

bin/macs2

 No newline at end of file

MACS_VERSION = "2.1.1.20160309"

MACS_VERSION = "2.1.2"

#MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"

FILTERDUP_VERSION = "1.0.0 20140616"

RANDSAMPLE_VERSION = "1.0.0 20120703"