Michael R. Crusoe pushed to branch upstream at Debian Med / macs
Commits: 2f85fecd by Michael R. Crusoe at 2026-05-14T10:26:08+02:00 New upstream version 3.0.4 - - - - - 158 changed files: - .github/workflows/build-and-test-MACS3-macos.yml - .github/workflows/build-and-test-MACS3-non-x64-others.yml - .github/workflows/build-and-test-MACS3-non-x64.yml - .github/workflows/build-and-test-MACS3-website.yml - .github/workflows/build-and-test-MACS3-x64.yml - − .github/workflows/publish-to-anaconda.yml - .github/workflows/publish-to-gh-with-sphinx.yml - .github/workflows/publish-to-pypi.yml - .gitignore - ChangeLog - LICENSE - MACS3/Commands/bdgbroadcall_cmd.py - MACS3/Commands/bdgcmp_cmd.py - MACS3/Commands/bdgdiff_cmd.py - MACS3/Commands/bdgopt_cmd.py - MACS3/Commands/bdgpeakcall_cmd.py - MACS3/Commands/callpeak_cmd.py - MACS3/Commands/callvar_cmd.py - MACS3/Commands/cmbreps_cmd.py - − MACS3/Commands/diffpeak_cmd.py - MACS3/Commands/filterdup_cmd.py - MACS3/Commands/hmmratac_cmd.py - MACS3/Commands/pileup_cmd.py - MACS3/Commands/predictd_cmd.py - MACS3/Commands/randsample_cmd.py - MACS3/Commands/refinepeak_cmd.py - + MACS3/IO/BAM.py - − MACS3/IO/BAM.pyx - MACS3/IO/BedGraphIO.pyx → MACS3/IO/BedGraphIO.py - MACS3/IO/OutputWriter.py - + MACS3/IO/Parser.py - − MACS3/IO/Parser.pyx - MACS3/IO/PeakIO.pyx → MACS3/IO/PeakIO.py - + MACS3/Signal/BedGraph.py - − MACS3/Signal/BedGraph.pyx - + MACS3/Signal/CallPeakUnit.py - − MACS3/Signal/CallPeakUnit.pyx - + MACS3/Signal/FixWidthTrack.py - − MACS3/Signal/FixWidthTrack.pyx - MACS3/Signal/HMMR_EM.pyx → MACS3/Signal/HMMR_EM.py - MACS3/Signal/HMMR_HMM.pyx → MACS3/Signal/HMMR_HMM.py - MACS3/Signal/HMMR_Signal_Processing.pyx → MACS3/Signal/HMMR_Signal_Processing.py - + MACS3/Signal/PairedEndTrack.py - − MACS3/Signal/PairedEndTrack.pyx - MACS3/Signal/PeakDetect.pyx → MACS3/Signal/PeakDetect.py - MACS3/Signal/PeakModel.pyx → MACS3/Signal/PeakModel.py - MACS3/Signal/PeakVariants.pyx → MACS3/Signal/PeakVariants.py - MACS3/Signal/Pileup.pyx → MACS3/Signal/Pileup.py - + MACS3/Signal/PileupV2.py - − MACS3/Signal/PileupV2.pyx - MACS3/Signal/PosReadsInfo.pyx → MACS3/Signal/PosReadsInfo.py - MACS3/Signal/Prob.pyx → MACS3/Signal/Prob.py - + MACS3/Signal/RACollection.pxd - MACS3/Signal/RACollection.pyx → MACS3/Signal/RACollection.py - MACS3/Signal/ReadAlignment.pyx → MACS3/Signal/ReadAlignment.py - MACS3/Signal/Region.pyx → MACS3/Signal/Region.py - MACS3/Signal/ScoreTrack.pyx → MACS3/Signal/ScoreTrack.py - MACS3/Signal/SignalProcessing.pyx → MACS3/Signal/SignalProcessing.py - MACS3/Signal/UnitigRACollection.pyx → MACS3/Signal/UnitigRACollection.py - MACS3/Signal/VariantStat.pyx → MACS3/Signal/VariantStat.py - MACS3/Utilities/Constants.py - MACS3/Utilities/Logger.py - MACS3/Utilities/OptValidator.py - README.md - bin/macs3 - − conda/macs3/meta.yaml - docs/source/conf.py - + docs/source/docs/FRAG.md - docs/source/docs/INSTALL.md - docs/source/docs/SAMBAMBAMPE.md - + docs/source/docs/api/commands/bdgbroadcall_cmd.rst - + docs/source/docs/api/commands/bdgcmp_cmd.rst - + docs/source/docs/api/commands/bdgdiff_cmd.rst - + docs/source/docs/api/commands/bdgopt_cmd.rst - + docs/source/docs/api/commands/bdgpeakcall_cmd.rst - + docs/source/docs/api/commands/callpeak_cmd.rst - + docs/source/docs/api/commands/callvar_cmd.rst - + docs/source/docs/api/commands/cmbreps_cmd.rst - + docs/source/docs/api/commands/filterdup_cmd.rst - + docs/source/docs/api/commands/hmmratac_cmd.rst - + docs/source/docs/api/commands/index.rst - + docs/source/docs/api/commands/pileup_cmd.rst - + docs/source/docs/api/commands/predictd_cmd.rst - + docs/source/docs/api/commands/randsample_cmd.rst - + docs/source/docs/api/commands/refinepeak_cmd.rst - + docs/source/docs/api/index.rst - + docs/source/docs/api/io/BAM.rst - + docs/source/docs/api/io/BedGraphIO.rst - + docs/source/docs/api/io/OutputWriter.rst - + docs/source/docs/api/io/Parser.rst - + docs/source/docs/api/io/PeakIO.rst - + docs/source/docs/api/io/index.rst - + docs/source/docs/api/signal/BedGraph.rst - + docs/source/docs/api/signal/CallPeakUnit.rst - + docs/source/docs/api/signal/FixWidthTrack.rst - + docs/source/docs/api/signal/HMMR_EM.rst - + docs/source/docs/api/signal/HMMR_HMM.rst - + docs/source/docs/api/signal/HMMR_Signal_Processing.rst - + docs/source/docs/api/signal/PairedEndTrack.rst - + docs/source/docs/api/signal/PeakDetect.rst - + docs/source/docs/api/signal/PeakModel.rst - + docs/source/docs/api/signal/PeakVariants.rst - + docs/source/docs/api/signal/Pileup.rst - + docs/source/docs/api/signal/PileupV2.rst - + docs/source/docs/api/signal/PosReadsInfo.rst - + docs/source/docs/api/signal/Prob.rst - + docs/source/docs/api/signal/RACollection.rst - + docs/source/docs/api/signal/ReadAlignment.rst - + docs/source/docs/api/signal/Region.rst - + docs/source/docs/api/signal/ScoreTrack.rst - + docs/source/docs/api/signal/SignalProcessing.rst - + docs/source/docs/api/signal/UnitigRACollection.rst - + docs/source/docs/api/signal/VariantStat.rst - + docs/source/docs/api/signal/index.rst - + docs/source/docs/api/utilities/Constants.rst - + docs/source/docs/api/utilities/Logger.rst - + docs/source/docs/api/utilities/OptValidator.rst - + docs/source/docs/api/utilities/index.rst - docs/source/docs/bdgdiff.md - docs/source/docs/callpeak.md - docs/source/docs/fileformats_index.md - docs/source/docs/hmmratac.md - docs/source/docs/pileup.md - docs/source/index.md - + notebooks/10k-PBMC-test/macs3-scATAC-pbmc-10k.ipynb - + notebooks/500-PBMC-test/macs3-scATAC-pbmc-500.ipynb - pyproject.toml - requirements.txt - setup.py - + test/barcodes.txt - test/cmdlinetest - test/jaccard.py - + test/standard_results_callpeak_frag/run_callpeak_frag_barcode_peaks.narrowPeak - + test/standard_results_callpeak_frag/run_callpeak_frag_peaks.narrowPeak - + test/standard_results_hmmratac/hmmratac_scatac_test_accessible_regions.narrowPeak - + test/test.fragments.tsv.gz - test/test_BAMBAI.py - test/test_BedGraph.py - test/test_BedGraphIO.py - test/test_CallPeakUnit.py - test/test_FixWidthTrack.py - test/test_HMMR_HMM.py - test/test_HMMR_poisson.py - test/test_PairedEndTrack.py - test/test_Parser.py - test/test_PeakDetect.py - test/test_PeakIO.py - test/test_PeakModel.py - test/test_Pileup.py - test/test_Prob.py - test/test_Region.py - test/test_ScoreTrack.py - test/test_SignalProcessing.py - test/test_online.py - + test/tiny.frag.tsv.gz - + test/yeast_500k_SRR1822137.barcode.txt - test/yeast_500k_SRR1822137.bedpe.gz - + test/yeast_500k_SRR1822137.frag.gz The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/macs/-/commit/2f85fecd6adf34ce75d5ffb3f9774484365a8be5 -- View it on GitLab: https://salsa.debian.org/med-team/macs/-/commit/2f85fecd6adf34ce75d5ffb3f9774484365a8be5 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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