MACS v2.2.4

The first release that is compatible with Python3

Features added

1. First Python3 version MACS2 released.

2. Version number 2.2.X will be used for MACS2 in Python3, in
   parallel to 2.1.X.

3. More comprehensive test.sh script to check the consistency of
   results from Python2 version and Python3 version.

4. Simplify setup.py script since the newest version transparently
   supports cython. And when cython is not installed by the user,
   setup.py can still compile using only C codes.

5. Fix Signal.pyx to use np.array instead of np.mat.

MACS v2.1.4

MACS version 2.1.4

• Features added

Github Actions is used together with Travis CI for testing and
deployment.

• Bugs fixed

  PR #322:

1. #318 Random score in bdgdiff output. It turns out the sum_v is
   not initialized as 0 before adding. Potential bugs are fixed in
   other functions in ScoreTrack and CallPeakUnit codes.

2. #321 Cython dependency in setup.py script is removed. And place
   'cythonzie' call to the correct position.

3. A typo is fixed in Github Actions script.

MACS v2.1.3.3

Redeploy to PyPI with only source code distribution. Plan to figure out how to build wheel for manylinux later.

MACS v2.1.3.2

Retry deployment. Keep only one setup script. Refer to v2.1.3 for ChangLog.

MACS v2.1.3

2019-09-19 Tao Liu [email protected]

* 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.

MACS v2.1.2.1

Note: this is a retagging of MACS v2.1.2 back on Oct 18, 2018. Due to a wrong upload to PyPI, then the re-uploaded package to PyPI for MACS v2.1.2 has been renamed as MACS2-2.1.2.1.tar.gz.

MACS2 v2.1.2

Please download from PyPI: https://pypi.org/project/MACS2/

MACS2 2.1.0 20150420 rc

Speed up and dispel some bugs. Note: this is ONLY a TAG for 2.1.0 release. The official release can be found at PyPI: https://pypi.python.org/pypi/MACS2/2.1.0.20150420

MACS2 2.1.0 20140616 rc

Note: this is ONLY a TAG for 2.1.0 release. The official release can be found at PyPI: https://pypi.python.org/pypi/MACS2/2.1.0.20140616