CMakeLists.txt
LICENSE
MANIFEST.in
README.md
__init__.py
build.sh
pepper.py
pepper_train.py
requirements.txt
setup.py
version.py
docker/Dockerfile
docker/pepper_wrapper.sh
img/.DS_Store
img/PEPPER_chemistry.png
img/PEPPER_error_rate.png
img/PEPPER_pipeline.svg
img/pip_logo.svg
img/terminal.svg
modules/htslib.cmake
modules/pybind11.cmake
modules/headers/pybind_api.h
modules/headers/dataio/bam_handler.h
modules/headers/dataio/fasta_handler.h
modules/headers/pileup_summary/summary_generator.h
modules/headers/realignment/aligner.h
modules/headers/realignment/simple_aligner.h
modules/headers/realignment/ssw.h
modules/headers/realignment/ssw_cpp.h
modules/python/AlignmentSummarizer.py
modules/python/DataStore.py
modules/python/DataStorePredict.py
modules/python/FileManager.py
modules/python/ImageGenerationUI.py
modules/python/Options.py
modules/python/Stitch.py
modules/python/StitchV2.py
modules/python/TextColor.py
modules/python/__init__.py
modules/python/call_consensus.py
modules/python/download_model.py
modules/python/make_images.py
modules/python/perform_stitch.py
modules/python/polish.py
modules/python/run_hyperband.py
modules/python/test_models.py
modules/python/train_models.py
modules/python/helper/__init__.py
modules/python/helper/generate_pileup_from_reads.py
modules/python/helper/hyperband_result.py
modules/python/models/ModelHander.py
modules/python/models/Seq2Seq_atn.py
modules/python/models/__init__.py
modules/python/models/dataloader.py
modules/python/models/dataloader_predict.py
modules/python/models/hyperband.py
modules/python/models/predict.py
modules/python/models/predict_distributed_cpu.py
modules/python/models/predict_distributed_gpu.py
modules/python/models/resnet.py
modules/python/models/simple_model.py
modules/python/models/test.py
modules/python/models/train.py
modules/python/models/train_distributed.py
modules/src/pybind_api.cpp
modules/src/dataio/bam_handler.cpp
modules/src/dataio/fasta_handler.cpp
modules/src/local_reassembly/aligner.cpp
modules/src/local_reassembly/simple_aligner.cpp
modules/src/local_reassembly/ssw.c
modules/src/local_reassembly/ssw_cpp.cpp
modules/src/pileup_summary/summary_generator.cpp
pepper_polish.egg-info/PKG-INFO
pepper_polish.egg-info/SOURCES.txt
pepper_polish.egg-info/dependency_links.txt
pepper_polish.egg-info/entry_points.txt
pepper_polish.egg-info/not-zip-safe
pepper_polish.egg-info/requires.txt
pepper_polish.egg-info/top_level.txt