.flake8
.gitignore
.pre-commit-config.yaml
CODE_OF_CONDUCT.md
LICENSE
README.md
main.spec
pyproject.toml
.github/ISSUE_TEMPLATE/add-a-new-reference.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/python-build-lint.yml
.github/workflows/python-publish.yml
.github/workflows/python-pyinstaller-linux.yml
.github/workflows/python-pyinstaller-win.yml
.vscode/launch.json
.vscode/settings.json
.vscode/tasks.json
DoubleHelix.egg-info/PKG-INFO
DoubleHelix.egg-info/SOURCES.txt
DoubleHelix.egg-info/dependency_links.txt
DoubleHelix.egg-info/entry_points.txt
DoubleHelix.egg-info/requires.txt
DoubleHelix.egg-info/top_level.txt
helix/VERSION.py
helix/__init__.py
helix/configuration.py
helix/main.py
helix/adapters/__init__.py
helix/adapters/alignment_map_file_info_adapter.py
helix/adapters/alignment_stats_adapter.py
helix/adapters/coverage_stats_adapter.py
helix/adapters/header_adapter.py
helix/adapters/index_stats_adapter.py
helix/adapters/reference_adapter.py
helix/alignment_map/__init__.py
helix/alignment_map/alignment_map_file.py
helix/alignment_map/alignment_map_header.py
helix/alignment_map/alignment_map_row.py
helix/alignment_map/alignment_stats_calculator.py
helix/alignment_map/depth_analyzer.py
helix/alignment_map/index_stats_calculator.py
helix/alignment_map/variant_caller.py
helix/data/__init__.py
helix/data/alignment_stats.py
helix/data/build.py
helix/data/chromosome_name_type.py
helix/data/coverage_stats.py
helix/data/file_type.py
helix/data/gender.py
helix/data/genome.py
helix/data/microarray_converter.py
helix/data/mitochondrial_model.py
helix/data/mitochondrial_model_type.py
helix/data/mitochondrial_name_type.py
helix/data/read_type.py
helix/data/sequence.py
helix/data/sequence_type.py
helix/data/sorting.py
helix/data/source.py
helix/data/tabular_data.py
helix/data/alignment_map/__init__.py
helix/data/alignment_map/alignment_map_file_info.py
helix/data/alignment_map/alignment_map_header_metadata.py
helix/data/alignment_map/alignment_map_header_program.py
helix/data/alignment_map/alignment_map_header_read_group.py
helix/data/alignment_map/alignment_map_header_sequence.py
helix/fasta/__init__.py
helix/fasta/fasta_letter_counter.py
helix/fasta/fasta_stats_files.py
helix/fasta/letter_run.py
helix/fasta/letter_run_buckets.py
helix/fasta/letter_run_collection.py
helix/fasta/reference.py
helix/fastq/__init__.py
helix/fastq/fastq_file.py
helix/files/__init__.py
helix/files/bgzip.py
helix/files/decompressor.py
helix/files/downloader.py
helix/files/file_type_checker.py
helix/files/gzip.py
helix/gui/WGSE-NG.pyproject
helix/gui/WGSE-NG.pyproject.user
helix/gui/__init__.py
helix/gui/form.ui
helix/gui/main.py
helix/gui/reference.ui
helix/gui/resources.qrc
helix/gui/table_dialog.py
helix/gui/ui_form.py
helix/gui/extract/extract_wizard.py
helix/gui/extract/format_selection.py
helix/gui/extract/microarray_selection.py
helix/gui/extract/sequence_selection.py
helix/gui/resources/logo.jpg
helix/gui/resources/logo_nXP_icon.ico
helix/metadata/__init__.py
helix/metadata/builds.json
helix/metadata/mtdna.json
helix/metadata/ploidy.txt
helix/metadata/references.json
helix/metadata/references_template.json
helix/metadata/sequencers.json
helix/metadata/sources.json
helix/metadata/bed_templates/37_wes.csv
helix/metadata/bed_templates/37_y_mt.csv
helix/metadata/bed_templates/38_wes.csv
helix/metadata/bed_templates/38_y_mt.csv
helix/metadata/bed_templates/__init__.py
helix/metadata/report_templates/__init__.py
helix/metadata/report_templates/table_macro.html
helix/metadata/report_templates/table_simple.html
helix/metadata/report_templates/table_tab.html
helix/microarray/__init__.py
helix/microarray/microarray_converter.py
helix/microarray/microarray_line_formatter.py
helix/microarray/raw_file.py
helix/mtDNA/CRS.fasta
helix/mtDNA/RSRS.fasta
helix/mtDNA/Yoruba.fasta
helix/mtDNA/__init__.py
helix/mtDNA/mt_dna.py
helix/mtDNA/rCRS.fasta
helix/naming/__init__.py
helix/naming/converter.py
helix/naming/lookup_tables.py
helix/naming/orderer.py
helix/progress/__init__.py
helix/progress/base_progress_calculator.py
helix/progress/process_io_monitor.py
helix/progress/simple_worker.py
helix/reference/__init__.py
helix/reference/genome_metadata_loader.py
helix/reference/repository_manager.py
helix/renderers/__init__.py
helix/renderers/csv_report.py
helix/renderers/html_aligned_file_report.py
helix/renderers/html_simple_table_report.py
helix/utility/__init__.py
helix/utility/check_prerequisites.py
helix/utility/external.py
helix/utility/installer.py
helix/utility/regions.py
helix/utility/samtools.py
helix/utility/sequencers.py
helix/utility/shortcut.py
helix/utility/unit_prefix.py
helix/utility/updater.py
test/__init__.py
test/fake_genome.fasta
test/test_buckets.py
test/test_fasta.py
test/test_fasta_dictionary.py
test/test_letter_run_collection.py
test/test_microarray_converter.py
test/test_raw_file.py
test/test_reference.py
test/test_sequence_canonicalizer.py
test/test_unknown_bases_stats.py
test/utility.py
tools/__init__.py
tools/fake_reference_genome_generator.py
tools/import_scanner.py
tools/last_file_export.py
tools/reference_stats.py