v3.0.0 Alpha 5 release

The fifth alpha release fixed an issue to correctly set CFLAG for older gcc compiler. Also, now it will use simde-no-test instead of simde as sub-module. The setup.py script has been cleaned up.

v3.0.0 Alpha 4 release

The alpha 4 release fixed an issue in 3.0.0a3 where the MANIFEST.in file doesn't include correct source code files, and fixed an issue so that --std=gnu99 cflag will be added to CFLAG while compiling fermi-lite codes.

v3.0.0 Alpha 3 release

The alpha 3 release fixed an issue in 3.0.0a2 where simde was not correctly included while uploading the package to PyPI through github action.

v3.0.0 Alpha 2 release

The second alpha release contains a newly added a callvar subcommand which can be used to call variants in given peak regions directly from ChIP-seq/ATAC-seq bam files with or without control. It also contains optimization in the MACS3.IO.Parser module to make reading gzipped BED files faster (20% less time).

v3.0.0 Alpha 1 release

v3.0.0 Alpha 1 release is to test the new reorganized codes and the new CI through GitHub Action which replaces TravisCI. The package should be uploaded to PyPI with twine.

MACS v2.2.7.1

hotfix

Add 'wheel' and 'pip' to pyproject.toml so that pip install can
work.

MACS v2.2.7 (broken pip pkg)

Bugs fixed

1. MACS2 has been tested on multiple architectures to make sure it
   can successfully generate consistent results. Currently the
   supported architectures are: AMD64, ARM64, i386, PPC64LE, and
   S390X. Thanks to @mr-c, @junaruga, and @tillea! Related to issue
   #340, #349, #351, and #359; to PR #348, #350, #360, #361, #367,
   and #370. The lesson is that if the project is built on Cython and
   is aimed at memory efficiency, we should specifically define all
   int/float types in pyx files such as int8_t or uint32_t using
   either libc or numpy (c version) instead of relying on Cython
   types such as short, long, double.

2. MACS2 setup script will check numpy and install numpy if
   necessary. PR #378, issue #364

3. bdgbroadcall command will correctly add the score column (5th
   column). The score (5th) column contains 10 times of the average
   score in the broad region. PR #373, issue #362

4. The missing test on bdgopt subcommand has been added. PR #363

5. The obsolete option --ratio from callpeak subcommand has
   been removed. PR #369, issue #366

6. Fixed the incorrect description in README on the 'maximum
   length of broad region is 4 times of d' to 'maximum gap for
   merging broad regions is 4 times of tag size by default'. PR #380,
   issue #365.

• Other

1. CODE OF CONDUCT document has been added to MACS2 github
   repository. PR #358

MACS v2.2.6

Speed up and other fixes

New Features

1. Speed up MACS2 with some programming tricks and code cleanup.

   The filter_dup function replaces separate_dups. The later one was
   implemented for potentially putting back duplicate reads in certain
   downstream analysis. However such analysis hasn't been implemented.
   Optimize the speed of writing bedGraph files. Optimize BAM and BAMPE
   parsing with pointer casting instead of python unpack.

2. The comment lines in the headers of BED or SAM files will be
   correctly skipped. However, MACS2 won't check comment lines in the
   middle of the file.

Bugs fixed

1. Cutoff-analysis in callpeak command. #341

2. Issues related to SAMParser and three ELAND Parsers are fixed. #347

Other

1. cmdlinetest script in test/ folder has been updated to: 1. test
   cutoff-analysis with callpeak cmd; 2. output the two lines before
   and after the error or warning message during testing; 3. output only
   the first 10 lines if the difference between test result and standard
   result can be found; 4. prockreport script monitor CPU time and
   memory usage in 1 second interval, providing a bit more accuracy.

2. Python3.5 support is removed. Now MACS2 requires Python>=3.6.

3. In the next release, we will remove the support for ELAND and BOWTIE
   format file, since SAM/BAM and BED format are more standard and flexible.

MACS v2.2.5

Python3 speed up

Features added

1. Github code only and Not included in MACS2 PyPI release New
   testing data for performance test. An subsampled ENCODE2 CTCF
   ChIP-seq dataset, including 5million ChIP reads and 5 million
   control reads, has been included in the test folder for testing
   CPU and memory usage (i.e. 5M test). Several related scripts ,
   including prockreport for output cpu memory usage, pyprofile
   and pyprofile_stat for debuging and profiling MACS2 codes, have
   been included.

2. Speed up pvalue-qvalue checkup (pqtable checkup) #335 #338.
   The old hashtable.pyx implementation copied from Pandas (very old
   version) doesn't work well in Python3+Cython. It slows down the
   pqtable checkup using the identical Cython codes as in
   v2.1.4. While running 5M test, the __getitem__ function in the
   hashtable.pyx took 3.5s with 37,382,037 calls in MACS2 v2.1.4, but
   148.6s with the same number of calls in MACS2 v2.2.4. As a
   consequence, the standard python dictionary implementation has
   replaced hashtable.pyx for pqtable checkup. Now MACS2 runs a bit
   faster than py2 version, but uses a bit more memory. In general,
   v2.2.5 can finish 5M reads test in 20% less time than MACS2
   v2.1.4, but use 15% more memory.

Bug fixed

1. More Python3 related fixes, e.g. the return value of keys from
   py3 dict. #333 #337

Note: The Github release package grows bigger since more testing
data have been included.

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.