MACS3 v3.0.2

What's New

• hmmratac poison emission added. #635
• hmmratac output in narrowPeak format
• cutoff-analysis feature enhanced. #636 #642
• hmmratac memory usage optimized #628 #640
• file format to be more compatible with UCSC browser #653
• Use -O3 instead of -Ofast for compatibility. #637
• Update instruction to install macs3 through conda/bioconda
• Reorganize MACS3 docs and publish through https://macs3-project.github.io/MACS
• Add documents for various file formats used in MACS3.

What's Changed (automatically generated log)

• explictly use Python version 3 by @mr-c in #623
• fix SyntaxWarning by marking a regex as such by @mr-c in #624
• Feat/macs3/output vers libs ga by @taoliu in #625
• Feat/macs3/unittest hmm by @taoliu in #627
• Fix spelling typos found by lintian by @mr-c in #629
• use CC instead of gcc by @bgruening in #630
• Use trusted publishing to upload package to pypi by @taoliu in #632
• Feat/macs3/hmmlearn0.3.2 by @taoliu in #631
• Feat/macs3/hmm poisson by @philippadoherty in #635
• [Feat/macs3/memory consumption] To address the memory usage issue of hmmratac by @taoliu in #640
• Documentation update and refine cutoff-analysis for hmmratac by @taoliu in #642
• Feat/macs3/narrowpeak by @taoliu in #645
• Doc/macs3/3.0.2 for v3.0.2 release by @taoliu in #657

Full Changelog: v3.0.1...v3.0.2

MACS3 v3.0.1

What's Changed

• fix labels for signal files from hmmratac by @philippadoherty in #611
• remove cython from setup.py requirements by @taoliu in #612
• documentation with Sphinx by @taoliu in #618
• Jaccard Index method to test similarity of outputs by @taoliu in #619
• patch hmmlearn, fix dependencies by @taoliu in #620

Full Changelog: https://github.com/macs3-project/MACS/blob/release/macs3/3.0.1/ChangeLog

MACS3 v3.0.0

First release of MACS3 (v3.0.0). Compared with the previous v3.0.0b3, changes are:

1. Cython 3 support #579
2. BEDPE support in hmmratac #580
3. correct libm support #587
4. removal of the requirement of pip and wheel #589
5. rewritten and reorganized documentation #597

Check other updates in MACS3 so far in previous beta/alpha releases and the ChangeLog file.

v3.0.0 beta 3 release

The third beta version of MACS3, addressing the Cython issue and adding more HMMRATAC options.

• New features from beta2:

1. HMMRATAC module

   --modelonly option: only generate HMM model and quit

   -t or --training: customized training regions can be provided through this option.

   --min-frag-p: exclude fragments with abnormal fragment length while generating four signal tracks. #577 Check macs3 hmmratac -h.

2. testing for Mac OS12 is added.

3. We require Cython 0.29.*. The new Cython3 will break our codes. We will adopt Cython3 later. #574

MACS2 v2.2.9.1

Since Cython has a major upgrade to 3.0, previous MACS2 can't be automatically installed through pip. Now we changed some requirements for dependencies: Python: 3.7 to 3.11, Cython 0.29.*, and Numpy >=0.19. The MACS3 setup.py script has been borrowed into MACS2 codes. Also, we tested MACS2 on Mac OS12 through Github Actions as well.

Thank @jemajet! #569

(overwrite the previous v2.2.9 since I forgot to include some changes to the documentation.)

v3.0.0 beta 2 release

MACS3 beta 2 release includes some improvements on hmmratac command. We've added the cutoff-analysis feature as in callpeak subcommand to hmmratac. It will provide help for users to decide the correct cutoff for training HMM. We also add the memory usage display to the runtime message. Also, we brought back GitHub Action testing for s390x, power64le, and armv7. We will work on rest of the documentation for the next release.

MACS2 v2.2.8

Now support Python 3.6-3.11, and newer numpy and cython, tested on x86 and ARM. Please note that .c files from cython pyx files have been removed from the package. They should be regenerated during installation so Cython is required.

v3.0.0 beta 1 release

MACS3 beta 1 release includes the new hmmratac command. We rewrote the HMMRATAC (Tarbell 2019) idea in Python. Now all the functions for MACS3 release is ready. We plan to do some optimization and tweaking on hmmratac feature in the next beta release and finish the documentation.

v3.0.0 Alpha 7 release

Alpha 7 provides support for BAI index of BAM file so that we can use the original BAM file instead of a subset BAM file for callvar command. Also, we fixed bugs related to #497 #498 (python 3.10 support) and #501 #502 (missing header line).

v3.0.0 Alpha 6 release

Alpha 6 release fixes an issue during building the paired-peak model #442. Also, now MACS3 uses SIMde v0.7.0. #437