LICENSE
MANIFEST.in
README.md
VERSION
changelog.md
isoquant.py
isoquant_detect_barcodes.py
isoquant_visualize.py
pyproject.toml
requirements.txt
requirements_tests.txt
isoquant.egg-info/PKG-INFO
isoquant.egg-info/SOURCES.txt
isoquant.egg-info/dependency_links.txt
isoquant.egg-info/entry_points.txt
isoquant.egg-info/requires.txt
isoquant.egg-info/top_level.txt
src/__init__.py
src/alignment_info.py
src/alignment_processor.py
src/assignment_aggregator.py
src/assignment_io.py
src/assignment_loader.py
src/cage_finder.py
src/common.py
src/convert_grouped_counts.py
src/correction_stats.py
src/dataset_processor.py
src/error_codes.py
src/exon_corrector.py
src/file_naming.py
src/file_utils.py
src/gene_info.py
src/gene_model.py
src/graph_based_model_construction.py
src/gtf2db.py
src/id_policy.py
src/illumina_exon_corrector.py
src/input_data_storage.py
src/intron_graph.py
src/isoform_assignment.py
src/junction_comparator.py
src/long_read_assigner.py
src/long_read_counter.py
src/long_read_profiles.py
src/modes.py
src/multimap_resolver.py
src/parallel_workers.py
src/plot_output.py
src/polya_finder.py
src/polya_verification.py
src/post_process.py
src/process_dict.py
src/processed_read_manager.py
src/read_groups.py
src/read_mapper.py
src/serialization.py
src/short_reads.py
src/short_utils.py
src/stats.py
src/string_pools.py
src/table_splitter.py
src/transcript_printer.py
src/barcode_calling/__init__.py
src/barcode_calling/common.py
src/barcode_calling/detect_barcodes.py
src/barcode_calling/umi_filtering.py
src/barcode_calling/callers/__init__.py
src/barcode_calling/callers/base.py
src/barcode_calling/callers/curio.py
src/barcode_calling/callers/extraction_result.py
src/barcode_calling/callers/molecule_structure.py
src/barcode_calling/callers/protocol.py
src/barcode_calling/callers/stereo.py
src/barcode_calling/callers/tenx.py
src/barcode_calling/callers/universal_extraction.py
src/barcode_calling/indexers/__init__.py
src/barcode_calling/indexers/base.py
src/barcode_calling/indexers/shared_memory.py
src/barcode_calling/indexers/two_bit.py
tests/__init__.py
tests/console_test.py
tests/test_alignment_info.py
tests/test_barcode2barcode.py
tests/test_barcode_callers.py
tests/test_barcode_common.py
tests/test_barcode_detectors.py
tests/test_ci_config.py
tests/test_common.py
tests/test_common_utilities.py
tests/test_enum_stats.py
tests/test_file_naming.py
tests/test_file_utils.py
tests/test_gene_info.py
tests/test_get_path_to_program.py
tests/test_id_distributor.py
tests/test_illumina_exon_corrector.py
tests/test_intron_graph.py
tests/test_iso_quant_mode.py
tests/test_junction_comparator.py
tests/test_kmer_indexer.py
tests/test_long_read_assigner.py
tests/test_long_read_profile.py
tests/test_molecule_structure.py
tests/test_polya_cage_finder.py
tests/test_read_groups.py
tests/test_serialization.py
tests/test_shared_mem_index.py
tests/test_string_pools.py
tests/test_umi_filtering.py
tests/test_universal_extraction.py
tests/simple_data/chr9.4M.Illumina.bam
tests/simple_data/chr9.4M.Illumina.bam.bai
tests/simple_data/chr9.4M.fa.gz
tests/simple_data/chr9.4M.fa.gz.fai
tests/simple_data/chr9.4M.gtf.gz
tests/simple_data/chr9.4M.ont.sim.fq.gz
tests/simple_data/chr9.4M.ont.sim.polya.bam
tests/simple_data/chr9.4M.ont.sim.polya.bam.bai
tests/simple_data/chr9.4M.ont.sim.read_groups.tsv
tests/simple_data/chr9.4M.yaml