.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE.md
README.md
environment.yml
pyproject.toml
requirements.txt
.github/workflows/python-package.yml
barcode_validator/__init__.py
barcode_validator/__main__.py
barcode_validator/_version.py
barcode_validator/cli.py
barcode_validator/constants.py
barcode_validator/criteria.py
barcode_validator/dna_analysis_result.py
barcode_validator/orchestrator.py
barcode_validator.egg-info/PKG-INFO
barcode_validator.egg-info/SOURCES.txt
barcode_validator.egg-info/dependency_links.txt
barcode_validator.egg-info/requires.txt
barcode_validator.egg-info/top_level.txt
barcode_validator/hmm_files/COI-5P.hmm
barcode_validator/hmm_files/__init__.py
barcode_validator/idservices/__init__.py
barcode_validator/idservices/bold.py
barcode_validator/idservices/factory.py
barcode_validator/idservices/idservice.py
barcode_validator/idservices/ncbi.py
barcode_validator/resolvers/__init__.py
barcode_validator/resolvers/bold.py
barcode_validator/resolvers/factory.py
barcode_validator/resolvers/ncbi.py
barcode_validator/resolvers/nsr.py
barcode_validator/resolvers/taxonomy.py
barcode_validator/validators/__init__.py
barcode_validator/validators/factory.py
barcode_validator/validators/non_coding.py
barcode_validator/validators/protein_coding.py
barcode_validator/validators/structural.py
barcode_validator/validators/taxonomic.py
barcode_validator/validators/validator.py
config/config.yml
config/benchmarking/16_test_config.yml
config/benchmarking/1_test_config.yml
config/benchmarking/2_test_config.yml
config/benchmarking/32_test_config.yml
config/benchmarking/4_test_config.yml
config/benchmarking/8_128_test_config.yml
config/benchmarking/8_256_test_config.yml
config/benchmarking/8_512_test_config.yml
config/benchmarking/8_64_test_config.yml
config/benchmarking/8_test_config.yml
config/benchmarking/test_config.yml
data/README.md
examples/BGE00001_00002_skim2phylo_cox1.fasta
examples/BGE00001_00002_skim2phylo_cox1.log
examples/BGE00001_00002_skim2phylo_cox1.tsv
examples/BGENL1147-24_cns
examples/Bioinformaticians_Hack_Day_filter_on_identification.out.tsv
examples/Bioinformaticians_Hack_Day_filter_on_identification.tsv
examples/Bioinformaticians_Hack_Day_filter_on_identification.tsv.log
examples/COI-5P.hmm
examples/README.md
examples/bold.xlsx
examples/cox1_concat_con.fasta
examples/cox1_concat_con.log
examples/cox1_concat_con.tsv
examples/empty_seq.fa
examples/input_Geneious_example.fasta
examples/mge.fa
examples/mge_meta.fa
examples/output_Geneious_example.fasta
examples/structval.tsv
examples/summary_stats.csv
examples/169_cns_mod/BGE00169-NC_cns.fas
examples/169_cns_mod/BGENL191-23_cns.fas
examples/169_cns_mod/BGENL192-23_cns.fas
examples/169_cns_mod/BGENL193-23_cns.fas
examples/169_cns_mod/BGENL194-23_cns.fas
examples/169_cns_mod/BGENL195-23_cns.fas
examples/169_cns_mod/BGENL196-23_cns.fas
examples/169_cns_mod/BGENL197-23_cns.fas
examples/169_cns_mod/BGENL198-23_cns.fas
examples/169_cns_mod/BGENL199-23_cns.fas
examples/169_cns_mod/BGENL200-23_cns.fas
examples/169_cns_mod/BGENL201-23_cns.fas
examples/169_cns_mod/BGENL202-23_cns.fas
examples/169_cns_mod/BGENL203-23_cns.fas
examples/169_cns_mod/BGENL204-23_cns.fas
examples/169_cns_mod/BGENL205-23_cns.fas
examples/169_cns_mod/BGENL206-23_cns.fas
examples/169_cns_mod/BGENL207-23_cns.fas
examples/169_cns_mod/BGENL208-23_cns.fas
examples/169_cns_mod/BGENL209-23_cns.fas
examples/169_cns_mod/BGENL210-23_cns.fas
examples/169_cns_mod/BGENL211-23_cns.fas
examples/169_cns_mod/BGENL212-23_cns.fas
examples/169_cns_mod/BGENL213-23_cns.fas
examples/169_cns_mod/BGENL214-23_cns.fas
examples/169_cns_mod/BGENL215-23_cns.fas
examples/169_cns_mod/BGENL216-23_cns.fas
examples/169_cns_mod/BGENL217-23_cns.fas
examples/169_cns_mod/BGENL218-23_cns.fas
examples/169_cns_mod/BGENL219-23_cns.fas
examples/169_cns_mod/BGENL220-23_cns.fas
examples/169_cns_mod/BGENL221-23_cns.fas
examples/169_cns_mod/BGENL222-23_cns.fas
examples/169_cns_mod/BGENL223-23_cns.fas
examples/169_cns_mod/BGENL224-23_cns.fas
examples/169_cns_mod/BGENL225-23_cns.fas
examples/169_cns_mod/BGENL226-23_cns.fas
examples/169_cns_mod/BGENL227-23_cns.fas
examples/169_cns_mod/BGENL228-23_cns.fas
examples/169_cns_mod/BGENL229-23_cns.fas
examples/169_cns_mod/BGENL230-23_cns.fas
examples/169_cns_mod/BGENL231-23_cns.fas
examples/169_cns_mod/BGENL232-23_cns.fas
examples/169_cns_mod/BGENL233-23_cns.fas
examples/169_cns_mod/BGENL234-23_cns.fas
examples/169_cns_mod/BGENL235-23_cns.fas
examples/169_cns_mod/BGENL236-23_cns.fas
examples/169_cns_mod/BGENL237-23_cns.fas
examples/169_cns_mod/BGENL238-23_cns.fas
examples/169_cns_mod/BGENL239-23_cns.fas
examples/169_cns_mod/BGENL240-23_cns.fas
examples/169_cns_mod/BGENL241-23_cns.fas
examples/169_cns_mod/BGENL242-23_cns.fas
examples/169_cns_mod/BGENL243-23_cns.fas
examples/169_cns_mod/BGENL244-23_cns.fas
examples/169_cns_mod/BGENL245-23_cns.fas
examples/169_cns_mod/BGENL246-23_cns.fas
examples/169_cns_mod/BGENL247-23_cns.fas
examples/169_cns_mod/BGENL248-23_cns.fas
examples/169_cns_mod/BGENL249-23_cns.fas
examples/169_cns_mod/BGENL250-23_cns.fas
examples/169_cns_mod/BGENL251-23_cns.fas
examples/169_cns_mod/BGENL252-23_cns.fas
examples/169_cns_mod/BGENL253-23_cns.fas
examples/169_cns_mod/BGENL254-23_cns.fas
examples/169_cns_mod/BGENL255-23_cns.fas
examples/169_cns_mod/BGENL256-23_cns.fas
examples/169_cns_mod/BGENL257-23_cns.fas
examples/169_cns_mod/BGENL258-23_cns.fas
examples/169_cns_mod/BGENL259-23_cns.fas
examples/169_cns_mod/BGENL260-23_cns.fas
examples/169_cns_mod/BGENL261-23_cns.fas
examples/169_cns_mod/BGENL262-23_cns.fas
examples/169_cns_mod/BGENL263-23_cns.fas
examples/169_cns_mod/BGENL264-23_cns.fas
examples/169_cns_mod/BGENL265-23_cns.fas
examples/169_cns_mod/BGENL266-23_cns.fas
examples/169_cns_mod/BGENL267-23_cns.fas
examples/169_cns_mod/BGENL268-23_cns.fas
examples/169_cns_mod/BGENL269-23_cns.fas
examples/169_cns_mod/BGENL270-23_cns.fas
examples/169_cns_mod/BGENL271-23_cns.fas
examples/169_cns_mod/BGENL272-23_cns.fas
examples/169_cns_mod/BGENL273-23_cns.fas
examples/169_cns_mod/BGENL274-23_cns.fas
examples/169_cns_mod/BGENL275-23_cns.fas
examples/169_cns_mod/BGENL276-23_cns.fas
examples/169_cns_mod/BGENL277-23_cns.fas
examples/169_cns_mod/BGENL278-23_cns.fas
examples/169_cns_mod/BGENL279-23_cns.fas
examples/169_cns_mod/BGENL280-23_cns.fas
examples/169_cns_mod/BGENL281-23_cns.fas
examples/169_cns_mod/BGENL282-23_cns.fas
examples/169_cns_mod/BGENL283-23_cns.fas
examples/169_cns_mod/BGENL284-23_cns.fas
examples/169_cns_mod/BGENL285-23_cns.fas
examples/rich_set/mge_fastp_r13s100_nocontam.csv
examples/rich_set/mge_fastp_r13s100_nocontam.fasta
examples/rich_set/mge_fastp_r13s100_nocontam.yaml
examples/tsv_explorer/app.R
examples/tsv_explorer/rsconnect.dcf
tests/test_blast.py
tests/test_bold_enrichment.py
tests/test_bold_id.py
tests/test_cli.py
tests/test_coding.py
tests/test_idservicefactory.py
tests/test_io.py
tests/test_marker_criteria.py
tests/test_merge.py
tests/test_ncbi_exptax.py
tests/test_nsr_enrichment.py
tests/test_result.py
tests/test_structural.py
tests/test_structval.py
tests/data/BGE00146_MGE-BGE_r1_1.3_1.5_s50_100.fasta
tests/data/bold.xlsx
tests/data/config.yml
tests/data/csc_sample.tsv
tests/data/nsr-20250207.dwca.zip
tests/data/structval_early_stop.fasta
tests/data/structval_ncbi.tsv
tests/data/structval_nsr.tsv
tests/data/tmp_o8h137e.fasta.tsv
tests/data/hmm_profiles/COI-5P.hmm