LICENCE.txt
MANIFEST.in
README.rst
setup.py
megalodon/__init__.py
megalodon/__main__.py
megalodon/_decode.pyx
megalodon/_version.py
megalodon/aggregate.py
megalodon/backends.py
megalodon/calibration.py
megalodon/fast5_io.py
megalodon/logging.py
megalodon/mapping.py
megalodon/megalodon.py
megalodon/megalodon_helper.py
megalodon/megalodon_multiprocessing.py
megalodon/mods.py
megalodon/signal_mapping.py
megalodon/variants.py
megalodon.egg-info/PKG-INFO
megalodon.egg-info/SOURCES.txt
megalodon.egg-info/dependency_links.txt
megalodon.egg-info/entry_points.txt
megalodon.egg-info/not-zip-safe
megalodon.egg-info/requires.txt
megalodon.egg-info/top_level.txt
megalodon/model_data/dna_r10.3_450bps_fast.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r10.3_450bps_fast.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r10.3_450bps_fast_prom.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r10.3_450bps_fast_prom.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r10.3_450bps_hac.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r10.3_450bps_hac.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r10.3_450bps_hac_prom.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r10.3_450bps_hac_prom.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_fast.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_fast.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_fast_prom.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_fast_prom.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_hac.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_hac.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_hac_prom.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_hac_prom.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg/megalodon_mod_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac_prom.cfg/megalodon_mod_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac_prom.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac_prom.cfg/megalodon_variant_calibration.npz
megalodon/model_data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac_prom.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/res_dna_r103_prom_modbases_5mC_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r103_prom_modbases_5mC_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases-all-context_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases-all-context_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases-all-context_v001.cfg/megalodon_variant_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases-all-context_v001.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases_5mC_5hmC_CpG_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases_5mC_5hmC_CpG_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases_5mC_5hmC_CpG_v001.cfg/megalodon_variant_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases_5mC_5hmC_CpG_v001.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases_5mC_CpG_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases_5mC_CpG_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases_5mC_CpG_v001.cfg/megalodon_variant_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases_5mC_CpG_v001.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/res_dna_r941_min_modbases_5mC_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_min_modbases_5mC_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_prom_modbases_5mC_CpG_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_prom_modbases_5mC_CpG_v001.cfg/megalodon_mod_calibration.pdf
megalodon/model_data/res_dna_r941_prom_modbases_5mC_CpG_v001.cfg/megalodon_variant_calibration.npz
megalodon/model_data/res_dna_r941_prom_modbases_5mC_CpG_v001.cfg/megalodon_variant_calibration.pdf
megalodon/model_data/res_dna_r941_prom_modbases_5mC_v001.cfg/megalodon_mod_calibration.npz
megalodon/model_data/res_dna_r941_prom_modbases_5mC_v001.cfg/megalodon_mod_calibration.pdf
megalodon_extras/__init__.py
megalodon_extras/__main__.py
megalodon_extras/_extras_parsers.py
megalodon_extras/aggregate_run.py
megalodon_extras/calibrate_generate_modified_base_stats.py
megalodon_extras/calibrate_generate_variant_stats.py
megalodon_extras/calibrate_merge_modified_bases.py
megalodon_extras/calibrate_modified_bases.py
megalodon_extras/calibrate_variants.py
megalodon_extras/merge_aggregated_modified_bases.py
megalodon_extras/merge_modified_bases.py
megalodon_extras/merge_variants.py
megalodon_extras/modified_bases_create_ground_truth.py
megalodon_extras/modified_bases_create_motif_bed.py
megalodon_extras/modified_bases_describe_alphabet.py
megalodon_extras/modified_bases_estimate_threshold.py
megalodon_extras/modified_bases_index_database.py
megalodon_extras/modified_bases_per_site_thresholds.py
megalodon_extras/modified_bases_split_by_motif.py
megalodon_extras/modified_bases_update_database.py
megalodon_extras/per_read_text_modified_bases.py
megalodon_extras/per_read_text_variants.py
megalodon_extras/phase_variants_extract_haplotype_reads.py
megalodon_extras/phase_variants_merge_haploid_variants.py
megalodon_extras/phase_variants_whatshap_filter.py
megalodon_extras/validate_aggregated_modified_bases.py
megalodon_extras/validate_compare_modified_bases.py
megalodon_extras/validate_results.py
megalodon_extras/variants_atomize.py
megalodon_extras/variants_heterozygous_factor.py
megalodon_extras/variants_index_database.py
megalodon_extras/variants_resolve.py
test/test_api.py