├── .circleci └── installHDF5.sh ├── .gitignore ├── CHANGELOG ├── LICENSES.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── bamboo_build.sh ├── bin ├── copyIpdSummaryDataset.py ├── hdf2npz.py ├── testShared.py └── writeSummaryToCmp.py ├── circle.yml ├── doc ├── Makefile ├── conf.py ├── index.rst ├── make.bat ├── manual.rst ├── regional_detection_manual.rst └── whitepaper │ ├── ecoli-roc.png │ ├── kinetics.bib │ ├── kinetics.pdf │ ├── kinetics.tex │ ├── logo.jpg │ └── position-influence.png ├── kineticsTools ├── BasicLdaEnricher.py ├── KineticWorker.py ├── MedakaLdaEnricher.py ├── MixtureEstimationMethods.py ├── ModificationDecode.py ├── MultiSiteCommon.py ├── MultiSiteDetection.py ├── PositiveControlEnricher.py ├── ReferenceUtils.py ├── ResultWriter.py ├── WorkerProcess.py ├── __init__.py ├── internal │ └── __init__.py ├── ipdModel.py ├── ipdSummary.py ├── loader.py ├── pipelineTools.py ├── resources │ ├── P6-C4.npz.gz │ ├── SP2-C2.npz.gz │ ├── SP3-C3.npz.gz │ └── unknown.npz.gz ├── sharedArray.py ├── summarizeModifications.py ├── tasks │ ├── __init__.py │ └── gather_bigwig.py └── tree_predict.c ├── pytest.ini ├── setup.py ├── strand-conventions.txt └── test ├── conftest.py ├── cram ├── detection_bam.t ├── detection_bam_dataset.t ├── detection_bam_lossless.t ├── extra │ └── bigwig.t ├── long_running │ ├── README.txt │ ├── detect_and_identify_Bsub.t │ ├── detect_and_identify_Cagg.t │ ├── detect_and_identify_Hpyl.t │ ├── detect_and_identify_Mjan.t │ ├── run_jenkins.sh │ └── run_on_cluster.py ├── methyl-fraction-identify.t.off ├── portability.sh └── version.t ├── data └── lambda │ ├── reference.info.xml │ └── sequence │ ├── lambda.fasta │ └── lambda.fasta.fai ├── detectionMethylFractionTest.py ├── test_ReferenceUtils.py ├── test_gather_bigwig.py ├── test_integration.py ├── test_ipdModel.py ├── test_loader.py ├── test_outputs.py └── test_summarize_modifications.py /.circleci/installHDF5.sh: 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