CMakeLists.txt
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
docker/Dockerfile
img/PEPPER_DeepVariant.png
img/PEPPER_chemistry.png
img/PEPPER_error_rate.png
img/PEPPER_pipeline.svg
img/pFDA_awards.png
img/pip_logo.svg
img/terminal.svg
pepper/__init__.py
pepper/pepper.py
pepper/pepper_train.py
pepper/version.py
pepper/modules/__init__.py
pepper/modules/htslib.cmake
pepper/modules/pybind11.cmake
pepper/modules/headers/pybind_api.h
pepper/modules/headers/dataio/bam_handler.h
pepper/modules/headers/dataio/fasta_handler.h
pepper/modules/headers/pileup_summary/summary_generator.h
pepper/modules/headers/realignment/aligner.h
pepper/modules/headers/realignment/simple_aligner.h
pepper/modules/headers/realignment/ssw.h
pepper/modules/headers/realignment/ssw_cpp.h
pepper/modules/python/AlignmentSummarizer.py
pepper/modules/python/DataStore.py
pepper/modules/python/DataStorePredict.py
pepper/modules/python/FileManager.py
pepper/modules/python/ImageGenerationUI.py
pepper/modules/python/Options.py
pepper/modules/python/Stitch.py
pepper/modules/python/StitchV2.py
pepper/modules/python/__init__.py
pepper/modules/python/call_consensus.py
pepper/modules/python/download_model.py
pepper/modules/python/make_images.py
pepper/modules/python/perform_stitch.py
pepper/modules/python/polish.py
pepper/modules/python/run_hyperband.py
pepper/modules/python/test_models.py
pepper/modules/python/train_models.py
pepper/modules/python/helper/__init__.py
pepper/modules/python/helper/generate_pileup_from_reads.py
pepper/modules/python/helper/hyperband_result.py
pepper/modules/python/models/ModelHander.py
pepper/modules/python/models/Seq2Seq_atn.py
pepper/modules/python/models/__init__.py
pepper/modules/python/models/dataloader.py
pepper/modules/python/models/dataloader_predict.py
pepper/modules/python/models/hyperband.py
pepper/modules/python/models/predict.py
pepper/modules/python/models/predict_distributed_cpu.py
pepper/modules/python/models/predict_distributed_gpu.py
pepper/modules/python/models/resnet.py
pepper/modules/python/models/simple_model.py
pepper/modules/python/models/test.py
pepper/modules/python/models/train.py
pepper/modules/python/models/train_distributed.py
pepper/modules/src/pybind_api.cpp
pepper/modules/src/dataio/bam_handler.cpp
pepper/modules/src/dataio/fasta_handler.cpp
pepper/modules/src/local_reassembly/aligner.cpp
pepper/modules/src/local_reassembly/simple_aligner.cpp
pepper/modules/src/local_reassembly/ssw.c
pepper/modules/src/local_reassembly/ssw_cpp.cpp
pepper/modules/src/pileup_summary/summary_generator.cpp
pepper_hp/pepper_hp.py
pepper_hp/pepper_hp_train.py
pepper_hp/modules/headers/pybind_api.h
pepper_hp/modules/headers/dataio/bam_handler.h
pepper_hp/modules/headers/dataio/fasta_handler.h
pepper_hp/modules/headers/pileup_summary/summary_generator.h
pepper_hp/modules/headers/realignment/aligner.h
pepper_hp/modules/headers/realignment/simple_aligner.h
pepper_hp/modules/headers/realignment/ssw.h
pepper_hp/modules/headers/realignment/ssw_cpp.h
pepper_hp/modules/python/AlignmentSummarizer.py
pepper_hp/modules/python/CallVariant.py
pepper_hp/modules/python/CandidateFinder.py
pepper_hp/modules/python/DataStore.py
pepper_hp/modules/python/DataStorePredict.py
pepper_hp/modules/python/ExcludeContigs.py
pepper_hp/modules/python/FileManager.py
pepper_hp/modules/python/FindCandidates.py
pepper_hp/modules/python/ImageGenerationUI.py
pepper_hp/modules/python/MakeImages.py
pepper_hp/modules/python/MergeVCFs.py
pepper_hp/modules/python/MergeVCFsWithSimplify.py
pepper_hp/modules/python/Options.py
pepper_hp/modules/python/RunInference.py
pepper_hp/modules/python/Stitch.py
pepper_hp/modules/python/StitchV2.py
pepper_hp/modules/python/TestModule.py
pepper_hp/modules/python/TextColor.py
pepper_hp/modules/python/TrainModule.py
pepper_hp/modules/python/VcfWriter.py
pepper_hp/modules/python/helper/generate_pileup_from_reads.py
pepper_hp/modules/python/helper/get_phase_block_lengths.py
pepper_hp/modules/python/helper/hyperband_result.py
pepper_hp/modules/python/helper/merge_vcf_test.py
pepper_hp/modules/python/helper/test_vcf.py
pepper_hp/modules/python/helper/test_vcf_merge.py
pepper_hp/modules/python/models/ModelHander.py
pepper_hp/modules/python/models/Seq2Seq_atn.py
pepper_hp/modules/python/models/dataloader.py
pepper_hp/modules/python/models/dataloader_predict.py
pepper_hp/modules/python/models/hyperband.py
pepper_hp/modules/python/models/predict_cpu.py
pepper_hp/modules/python/models/predict_distributed_gpu.py
pepper_hp/modules/python/models/predict_fake.py
pepper_hp/modules/python/models/resnet.py
pepper_hp/modules/python/models/simple_model.py
pepper_hp/modules/python/models/test.py
pepper_hp/modules/python/models/train.py
pepper_hp/modules/python/models/train_distributed.py
pepper_hp/modules/src/pybind_api.cpp
pepper_hp/modules/src/candidate_finder/candidate_finder.cpp
pepper_hp/modules/src/dataio/bam_handler.cpp
pepper_hp/modules/src/dataio/fasta_handler.cpp
pepper_hp/modules/src/local_reassembly/aligner.cpp
pepper_hp/modules/src/local_reassembly/simple_aligner.cpp
pepper_hp/modules/src/local_reassembly/ssw.c
pepper_hp/modules/src/local_reassembly/ssw_cpp.cpp
pepper_hp/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
pepper_snp/__init__.py
pepper_snp/pepper_snp.py
pepper_snp/pepper_snp_train.py
pepper_snp/modules/headers/pybind_api.h
pepper_snp/modules/headers/dataio/bam_handler.h
pepper_snp/modules/headers/dataio/fasta_handler.h
pepper_snp/modules/headers/pileup_summary/summary_generator.h
pepper_snp/modules/headers/realignment/aligner.h
pepper_snp/modules/headers/realignment/simple_aligner.h
pepper_snp/modules/headers/realignment/ssw.h
pepper_snp/modules/headers/realignment/ssw_cpp.h
pepper_snp/modules/python/AlignmentSummarizer.py
pepper_snp/modules/python/CallVariant.py
pepper_snp/modules/python/CandidateFinder.py
pepper_snp/modules/python/DataStore.py
pepper_snp/modules/python/DataStorePredict.py
pepper_snp/modules/python/ExcludeContigs.py
pepper_snp/modules/python/FileManager.py
pepper_snp/modules/python/FindSNPCandidates.py
pepper_snp/modules/python/ImageGenerationUI.py
pepper_snp/modules/python/MakeImages.py
pepper_snp/modules/python/Options.py
pepper_snp/modules/python/RunHyperband.py
pepper_snp/modules/python/RunInference.py
pepper_snp/modules/python/Stitch.py
pepper_snp/modules/python/TestModule.py
pepper_snp/modules/python/TrainModule.py
pepper_snp/modules/python/VcfWriter.py
pepper_snp/modules/python/__init__.py
pepper_snp/modules/python/helper/generate_pileup_from_reads.py
pepper_snp/modules/python/helper/hyperband_result.py
pepper_snp/modules/python/models/ModelHander.py
pepper_snp/modules/python/models/Seq2Seq_atn.py
pepper_snp/modules/python/models/__init__.py
pepper_snp/modules/python/models/dataloader.py
pepper_snp/modules/python/models/dataloader_predict.py
pepper_snp/modules/python/models/hyperband.py
pepper_snp/modules/python/models/predict.py
pepper_snp/modules/python/models/predict_distributed_cpu.py
pepper_snp/modules/python/models/predict_distributed_gpu.py
pepper_snp/modules/python/models/resnet.py
pepper_snp/modules/python/models/simple_model.py
pepper_snp/modules/python/models/test.py
pepper_snp/modules/python/models/train.py
pepper_snp/modules/python/models/train_distributed.py
pepper_snp/modules/src/pybind_api.cpp
pepper_snp/modules/src/dataio/bam_handler.cpp
pepper_snp/modules/src/dataio/fasta_handler.cpp
pepper_snp/modules/src/local_reassembly/aligner.cpp
pepper_snp/modules/src/local_reassembly/simple_aligner.cpp
pepper_snp/modules/src/local_reassembly/ssw.c
pepper_snp/modules/src/local_reassembly/ssw_cpp.cpp
pepper_snp/modules/src/pileup_summary/summary_generator.cpp