MANIFEST.in
README.md
setup.py
densecall/LICENCE.txt
densecall/__init__.py
densecall/__main__.py
densecall/aligner.py
densecall/data.py
densecall/fast5.py
densecall/io.py
densecall/mod_util.py
densecall/multiprocessing.py
densecall/pod5.py
densecall/reader.py
densecall/requirements.txt
densecall/schedule.py
densecall/slow5.py
densecall/training.py
densecall/util.py
densecall.egg-info/PKG-INFO
densecall.egg-info/SOURCES.txt
densecall.egg-info/dependency_links.txt
densecall.egg-info/entry_points.txt
densecall.egg-info/not-zip-safe
densecall.egg-info/requires.txt
densecall.egg-info/top_level.txt
densecall/asr/__init__.py
densecall/asr/basecall.py
densecall/asr/ctcdecode.py
densecall/asr/model.py
densecall/asr/model_.py
densecall/asr/plot_attention_heatmap.py
densecall/cli/__init__.py
densecall/cli/accuracy.py
densecall/cli/basecaller.py
densecall/cli/convert.py
densecall/cli/lm.py
densecall/cli/rnalm.py
densecall/cli/sigmap.py
densecall/cli/to_taiyaki.py
densecall/cli/train.py
densecall/conformer/__init__.py
densecall/conformer/basecall.py
densecall/conformer/cgmlp.py
densecall/conformer/conv.py
densecall/conformer/criterion.py
densecall/conformer/flash.py
densecall/conformer/greedy_decode.py
densecall/conformer/linformer.py
densecall/conformer/modcall.py
densecall/conformer/model.py
densecall/conformer/modules.py
densecall/conformer/nn.py
densecall/conformer/optimize.py
densecall/conformer/reversible.py
densecall/conformer/util.py
densecall/lm/__init__.py
densecall/lm/backbone.py
densecall/lm/config.toml
densecall/lm/config_arm.toml
densecall/lm/lm.py
densecall/lm/model.py
densecall/lm/posttrain.py
densecall/lm/predict_genome.py
densecall/lm/pretrain.py
densecall/lm/schedule.py
densecall/lm/utils.py
densecall/models/configs/conformer.toml
densecall/models/configs/conformer_rna.toml
densecall/models/configs/hybrid_transformer.toml
densecall/models/configs/hybrid_transformer_dna.toml
densecall/rnalm/__init__.py
densecall/rnalm/analysis.py
densecall/rnalm/analyze_m6a_cls.py
densecall/rnalm/analyze_mask_sweep.py
densecall/rnalm/analyze_when_y_helps.py
densecall/rnalm/backbone.py
densecall/rnalm/cluster_boot.py
densecall/rnalm/compare_y_windows.py
densecall/rnalm/data_maker.py
densecall/rnalm/data_maker_m6a.py
densecall/rnalm/dna_vocab.py
densecall/rnalm/lmy.py
densecall/rnalm/make_m6a_cls_data.py
densecall/rnalm/make_ymask_variants.py
densecall/rnalm/model.py
densecall/rnalm/replicate_concordance.py
densecall/rnalm/schedule.py
densecall/rnalm/train_m6a_cls.py
densecall/rnalm/train_splice_m6a.py
densecall/rnalm/utils.py
densecall/rnalm/configs/configs_15tissue.yaml
densecall/rnalm/configs/configs_15tissue_m6a.yaml
densecall/rnalm/configs/configs_15tissue_small.yaml
densecall/rnalm/configs/configs_all_tissue.yaml
densecall/rnalm/configs/configs_all_tissue_m6a.yaml
densecall/rnalm/configs/configs_all_tissue_small.yaml
densecall/scripts/m6a_benchmark_complete.py
densecall/scripts/plot_m6a_comparison.py
densecall/work_asr_fast/__init__.py
densecall/work_asr_fast/arch_util.py
densecall/work_asr_fast/bn_fold.py
densecall/work_asr_fast/fuse_all.py
densecall/work_asr_fast/fuse_conformer.py
densecall/work_asr_fast/fuse_ln.py
densecall/work_asr_fast/fuse_model.py
densecall/work_asr_fast/fuse_silu.py
densecall/work_asr_fast/fused_ffn_4090.py
densecall/work_asr_fast/fused_ffn_cfm.py
densecall/work_asr_fast/fused_rotary.py
tests/test_structure.py