| HEAD | 880ab61 | Merge pull request #635 from macs3-project/feat/macs3/hmm_poisson Feat/macs3/hmm poisson | 28 March 2024, 19:29:44 UTC |
| refs/heads/add-code-of-conduct-1 | e413aac | Create CODE_OF_CONDUCT.md | 28 January 2020, 18:55:39 UTC |
| refs/heads/chore_documents | fa9a74f | Merge pull request #350 from taoliu/fix_test_signal_py38_dev Fix: test_Signal.py failure. Related to certain combinations of Python and Numpy | 19 December 2019, 15:28:09 UTC |
| refs/heads/doc/macs/license-2020 | 0869254 | Update LICENSE | 07 December 2020, 16:43:53 UTC |
| refs/heads/doc/macs3/3.0.0 | b904d8d | pilup cmd draft | 28 June 2023, 17:04:12 UTC |
| refs/heads/doc/macs3/3.0.0b4 | 9f25975 | add desc regarding windows. change development status | 14 November 2023, 21:44:33 UTC |
| refs/heads/doc/macs3/jekyll_equations | ea37e3e | update callvar.md;update workflow for building website | 05 December 2023, 17:51:05 UTC |
| refs/heads/doc/macs3/sphinx_migration | ef04fb3 | update build-and-test website workflow with Sphinx | 13 February 2024, 20:59:27 UTC |
| refs/heads/doc/macs3/update_march_2024 | 783f8c0 | update instructions for conda install | 28 March 2024, 20:02:33 UTC |
| refs/heads/doc_contributing | 2db0f0f | Merge pull request #386 from taoliu/fix_zeroDivision_383 The cutoff-analysis of CallPeakUnit has the same behavior as bdgpeakc… | 20 April 2020, 20:17:18 UTC |
| refs/heads/feat/macs3/build_without_cython | 2a27840 | bring branch up to speed from last PR Merge branch 'master' into feat/macs3/build_without_cython | 10 January 2024, 22:23:15 UTC |
| refs/heads/feat/macs3/callpeak_multiprocessing | eeec19f | only return extra pscore_dict | 07 December 2020, 04:01:56 UTC |
| refs/heads/feat/macs3/callvar | 5aedab9 | update README | 05 December 2020, 23:43:29 UTC |
| refs/heads/feat/macs3/callvar2 | 4a861d6 | Merge branch 'feat/macs3/callvar2' of github.com:macs3-project/MACS into feat/macs3/callvar2 | 04 March 2021, 16:30:43 UTC |
| refs/heads/feat/macs3/clipper | 79dfe5d | Clipper Add-On From JSB Lab | 21 November 2022, 21:16:01 UTC |
| refs/heads/feat/macs3/codecleanup | 4c9ad01 | do not build bdist_wheel | 04 December 2020, 16:53:43 UTC |
| refs/heads/feat/macs3/cram-support | 076ee83 | Merge pull request #576 from macs3-project/feat/macs3/hmmratac MACS3 b3 update `hmmratac` and `Cython` issue | 30 July 2023, 14:38:35 UTC |
| refs/heads/feat/macs3/diffpeak | 38d7d8b | quick fix: do not build bdist_wheel for pypi | 04 December 2020, 16:56:01 UTC |
| refs/heads/feat/macs3/hmm_poisson | 82917c4 | Include pushes to master - Merge branch 'master' into feat/macs3/hmm_poisson | 26 March 2024, 20:40:03 UTC |
| refs/heads/feat/macs3/hmmlearn0.3.2 | 9f91e6c | update versions of dependencies | 02 March 2024, 14:44:06 UTC |
| refs/heads/feat/macs3/hmmratac | d734ebd | Merge branch 'master' into feat/macs3/hmmratac | 30 July 2023, 01:59:52 UTC |
| refs/heads/feat/macs3/profile | 5810ddd | formatting | 17 February 2023, 19:19:41 UTC |
| refs/heads/feat/macs3/py312 | ef5b160 | revert to numpy > 1.19, test py 3.12 | 14 November 2023, 16:28:20 UTC |
| refs/heads/feat/macs3/pypi_trusted_publishing | ec8f2c5 | Update publish-to-pypi.yml | 02 March 2024, 15:59:02 UTC |
| refs/heads/feat/macs3/test_peak_overlap | c4e687e | make testing for armv7/ppc64le/s390x on-demmand in master branch only because it took too long to finish. we only keep aarch64 or arm v8 in the standard non-x86 test | 16 February 2024, 19:31:22 UTC |
| refs/heads/feat/macs3/unittest_hmm | 8adc427 | update standard prediction results | 27 February 2024, 18:54:56 UTC |
| refs/heads/feat_cykhash | 8bfb192 | try khash | 12 November 2020, 20:09:25 UTC |
| refs/heads/feat_optimize_write | 0829c4d | fix bug due to a debugging code | 07 November 2019, 13:12:30 UTC |
| refs/heads/feat_py3 | af91e93 | Another typo in travis.yml | 02 October 2019, 17:01:05 UTC |
| refs/heads/feat_speed_optimization | 46ec485 | rename pyprofile_stat script | 31 October 2019, 06:41:51 UTC |
| refs/heads/feat_speed_optimization2 | bc089ea | update temporary ChangeLog file | 05 November 2019, 18:21:25 UTC |
| refs/heads/feat_tweak_buffer_size | d4fc920 | Related to #313. Enable --buffer-size for filterdup, pileup, randsample, and refinepeak. Catch MemoryError and give suggestion to users. Update testing script to run 50k contigs file. Decrease filesize of the testing files of BAMPE and BEDPE. | 19 September 2019, 21:01:02 UTC |
| refs/heads/feat_wacs | 7cd205a | clean up | 24 September 2019, 18:52:32 UTC |
| refs/heads/fix/macs3/584_report_zero_reads | c21e1dd | Report error if no fragments (proper pair) can be read from input BAMPE file. #584 | 14 August 2023, 16:08:21 UTC |
| refs/heads/fix/macs3/cleanup | 5825e72 | clean functions' names | 12 September 2023, 18:18:40 UTC |
| refs/heads/fix/macs3/largechromosome | 291fae8 | Merge pull request #497 from ggraham/master accurate python version reporting in setup for python 3.10+ | 18 January 2022, 14:20:21 UTC |
| refs/heads/fix/macs3/python312numpy | 429f8f8 | Merge pull request #589 from tjni/clean-up-build-dependencies remove pip and wheel from build dependencies | 12 August 2023, 00:08:48 UTC |
| refs/heads/fix/macs3/signal_text | 6aca443 | fix labels for signals | 10 January 2024, 18:01:59 UTC |
| refs/heads/fix/macs3/test_numpy_version124 | 15d36d4 | try >=1.25 | 31 January 2024, 21:14:30 UTC |
| refs/heads/fix_BedGraph_keys | 907ac53 | get_chr_names will return set instead of list or key object | 30 October 2019, 16:20:10 UTC |
| refs/heads/fix_bdgbroadcall_score_display | dfcf9d2 | enable py3.6/3.7 tests under amd64 | 07 April 2020, 18:56:25 UTC |
| refs/heads/fix_bdgdiff_318 | 5ef8863 | Remove uploading to Test PyPI. Testing can't be done if Test PyPI doesn't allow filename reuse. | 30 September 2019, 18:19:12 UTC |
| refs/heads/fix_cutoffanalysis_341 | 19671c8 | add callpeak --cutoff-analysis to test script | 02 November 2019, 05:44:21 UTC |
| refs/heads/fix_predictd_support_bampe_bedpe | dc935e8 | fix test. fix typo in predictd_cmd | 13 April 2020, 21:12:36 UTC |
| refs/heads/fix_readme_365 | 810277d | update dockerfile | 11 April 2020, 04:51:35 UTC |
| refs/heads/fix_remove_ratio_option | f8328dd | remove --ratio from callpeak subcommand. #366 | 25 March 2020, 21:18:00 UTC |
| refs/heads/fix_setup_script_364 | aaa4b44 | use sys.executable to access pip module. | 09 April 2020, 17:00:35 UTC |
| refs/heads/fix_test_bdgopt | 0611f87 | add bdgopt test files | 04 March 2020, 06:00:19 UTC |
| refs/heads/fix_test_multiarch_precision | bc6dde4 | comment some unnecessary codes | 29 March 2020, 21:43:00 UTC |
| refs/heads/fix_test_signal_py38_dev | b1ea912 | Merge branch 'fix_test_signal_py38_dev' of github.com:taoliu/MACS into fix_test_signal_py38_dev | 18 February 2020, 15:51:50 UTC |
| refs/heads/fix_zeroDivision_383 | af166a9 | The cutoff-analysis of CallPeakUnit has the same behavior as bdgpeakcall, to skip cutoff without peaks | 20 April 2020, 19:33:02 UTC |
| refs/heads/macs_v1 | a662072 | Update OptValidator.py Fix link to PeakSplitter | 29 September 2016, 15:20:31 UTC |
| refs/heads/macs_v2 | b18703b | Merge pull request #590 from tjni/macs2-clean-up-build-dependencies macs2: remove pip and wheel from build dependencies | 12 August 2023, 00:06:12 UTC |
| refs/heads/master | 880ab61 | Merge pull request #635 from macs3-project/feat/macs3/hmm_poisson Feat/macs3/hmm poisson | 28 March 2024, 19:29:44 UTC |
| refs/heads/misc/macs3/reproduce_debian_med_testing_results | 1b240d7 | turn on testing for python3.9-3.12 | 18 February 2024, 22:30:45 UTC |
| refs/heads/release/macs3/3.0.0 | 27e4cb3 | change way to decide the open/nuc/bg states | 04 October 2022, 21:00:18 UTC |
| refs/heads/release/macs3/3.0.1 | 08b8608 | update conda badge | 23 February 2024, 05:43:07 UTC |
| refs/heads/release_v2.1.3 | bde2a92 | Revert usage of OutputWriter.py | 20 September 2019, 16:10:59 UTC |
| refs/heads/release_v2.1.4 | 85920ca | fallback using travis to release... | 30 September 2019, 21:50:53 UTC |
| refs/heads/release_v2.2.4 | e7df7b5 | Edit README. | 03 October 2019, 16:29:05 UTC |
| refs/heads/release_v2.2.5 | d612a00 | Update README and Changelog | 31 October 2019, 14:57:28 UTC |
| refs/heads/release_v2.2.6 | f7f0001 | Tiny input files for testing Parser.pyx. | 12 December 2019, 19:43:50 UTC |
| refs/heads/release_v2.2.7.1 | d5a46c1 | Merge pull request #543 from tyamadat/release_v2.2.7.1 Fix: typo in setup.py causing an error when installing v2.2.7.1 by pip | 13 February 2023, 21:17:05 UTC |
| refs/heads/release_v2.2.7.2 | d5a46c1 | Merge pull request #543 from tyamadat/release_v2.2.7.1 Fix: typo in setup.py causing an error when installing v2.2.7.1 by pip | 13 February 2023, 21:17:05 UTC |
| refs/tags/1.4beta | c0cb75e | first commit of MACS1.4beta | 02 March 2011, 19:52:27 UTC |
| refs/tags/2.1.0.20140616 | 38db9f5 | Update README.rst Minor update | 17 June 2014, 21:04:01 UTC |
| refs/tags/2015.4.20 | 7f46b06 | 2015.4.20 release | 20 April 2015, 18:38:41 UTC |
| refs/tags/v2 | 0976e34 | Add a bdgcmp script to calculate scores from two bedGraph files, then bdgpeakcall can be used to take the score bedGraph and call peaks with certain cutoff. | 10 June 2011, 20:14:15 UTC |
| refs/tags/v2.1.2 | 8939707 | Prepare release of 2.1.2 | 17 October 2018, 20:22:41 UTC |
| refs/tags/v2.1.3 | 7fc4c3f | Merge pull request #316 from taoliu/release_v2.1.3 Release v2.1.3 | 20 September 2019, 16:34:28 UTC |
| refs/tags/v2.1.3.2 | e2581dc | Remove usage of setup_w_cython.py. Require always generating c codes from pyx files during installation. | 20 September 2019, 18:09:40 UTC |
| refs/tags/v2.1.3.3 | 6e0a0fe | no bdist_wheel. Figure out how to do manylinux wheel later... | 20 September 2019, 19:48:41 UTC |
| refs/tags/v2.1.4 | 85920ca | fallback using travis to release... | 30 September 2019, 21:50:53 UTC |
| refs/tags/v2.2.4 | fff5f1d | Merge pull request #325 from taoliu/release_v2.2.4 Release v2.2.4 | 03 October 2019, 18:26:58 UTC |
| refs/tags/v2.2.5 | 7276a8d | Merge pull request #339 from taoliu/release_v2.2.5 Release v2.2.5 | 31 October 2019, 15:14:38 UTC |
| refs/tags/v2.2.6 | f72b84c | Merge pull request #345 from taoliu/release_v2.2.6 Release v2.2.6 | 12 December 2019, 20:35:53 UTC |
| refs/tags/v2.2.7 | e40d18b | fix bug in travis.yml; only call for deployment at amd64_py3.8 | 11 April 2020, 22:59:27 UTC |
| refs/tags/v2.2.7.1 | 00f489c | update changelog and readme.md | 12 April 2020, 00:00:15 UTC |
| refs/tags/v2.2.8 | f350e8c | test non-x64. use actions v3 | 12 May 2023, 20:37:52 UTC |
| refs/tags/v2.2.9 | ee14c18 | name workflows in MACS2 | 20 July 2023, 15:09:28 UTC |
| refs/tags/v2.2.9.1 | 1afcae6 | Update docs for v2.2.9.1 | 21 July 2023, 14:25:59 UTC |
| refs/tags/v3.0.0 | f9c6546 | clean up documents, changelog, readme | 15 November 2023, 16:09:23 UTC |
| refs/tags/v3.0.0a1 | 38d7d8b | quick fix: do not build bdist_wheel for pypi | 04 December 2020, 16:56:01 UTC |
| refs/tags/v3.0.0a2 | c692b32 | Merge pull request #427 from macs3-project/feat/macs3/parser_optimization Feat: MACS3 parser optimization; v3.0.0a2 ready | 07 December 2020, 13:34:44 UTC |
| refs/tags/v3.0.0a3 | d78344e | Update setup.py | 07 December 2020, 23:20:12 UTC |
| refs/tags/v3.0.0a4 | 11d0642 | Merge pull request #430 from macs3-project/fix/macs3/packaging_and_compiler Fix: add gnu99 to cflag; fix the manifest.in | 08 December 2020, 00:59:00 UTC |
| refs/tags/v3.0.0a5 | cbb4557 | Merge pull request #432 from macs3-project/fix/macs3/c_compiler_issues Fix: detect C compiler version | 09 December 2020, 08:14:17 UTC |
| refs/tags/v3.0.0a6 | b7fb06f | Merge pull request #446 from macs3-project/fix/macs3/peakmodel442 Fix: 0 pair for paired-peak model #442 | 08 February 2021, 15:29:47 UTC |
| refs/tags/v3.0.0a7 | 8a6cc81 | v3.0.0a7 release | 18 February 2022, 16:56:15 UTC |
| refs/tags/v3.0.0b1 | f830bcb | Merge pull request #527 from macs3-project/release/macs3/3.0.0 Release/macs3/3.0.0b1 | 05 October 2022, 14:31:56 UTC |
| refs/tags/v3.0.0b2 | 0c161d5 | update date in changelog and dev status in setup.py for PyPI | 23 June 2023, 21:29:21 UTC |
| refs/tags/v3.0.0b3 | 076ee83 | Merge pull request #576 from macs3-project/feat/macs3/hmmratac MACS3 b3 update `hmmratac` and `Cython` issue | 30 July 2023, 14:38:35 UTC |
| refs/tags/v3.0.1 | 3cfb5dc | Merge pull request #622 from macs3-project/release/macs3/3.0.1 Release/macs3/3.0.1 | 23 February 2024, 05:43:44 UTC |
