Rz-coder8848/moonbit-genbank/cmd/main

README
- ::messageGenBankError::message
- ::to_json_stringAlignmentSummary::to_json_string
- ::to_json_stringAnnotationSummary::to_json_string
- ::to_json_stringAssemblyResult::to_json_string
- ::to_json_stringBatchQualityReport::to_json_string
- ::to_textBatchQualityReport::to_text
- ::to_json_stringBatchSummary::to_json_string
- ::to_textBatchSummary::to_text
- ::to_json_stringCdsTranslationResult::to_json_string
- ::to_json_stringCodingSequenceReport::to_json_string
- ::to_tsvCodingSequenceReport::to_tsv
T
CodonTable
- ::to_json_stringCodonUsage::to_json_string
- ::to_json_stringCompositionReport::to_json_string
T
ContigOverlap
- ::to_json_stringCoordinateInterval::to_json_string
- ::to_textFastaIssue::to_text
- ::to_fastaFastaRecord::to_fasta
- ::to_json_stringFastaValidationReport::to_json_string
- ::overlapsFeature::overlaps
- ::qualifierFeature::qualifier
- ::to_genbank_headFeature::to_genbank_head
- ::to_json_stringFeature::to_json_string
- ::to_json_stringFeatureExtraction::to_json_string
- ::allFeatureIndex::all
- ::atFeatureIndex::at
- ::by_keyFeatureIndex::by_key
- ::by_keysFeatureIndex::by_keys
- ::by_qualifierFeatureIndex::by_qualifier
- ::contained_inFeatureIndex::contained_in
- ::countFeatureIndex::count
- ::keysFeatureIndex::keys
- ::overlappingFeatureIndex::overlapping
- ::positionsFeatureIndex::positions
- ::qualifier_namesFeatureIndex::qualifier_names
- ::summary_jsonFeatureIndex::summary_json
- ::with_qualifierFeatureIndex::with_qualifier
T
FeatureIndexEntry
- ::to_json_stringFeatureKeySummary::to_json_string
- ::to_json_stringFeatureProjection::to_json_string
- ::to_json_stringFeatureTableRow::to_json_string
- ::to_json_stringGlobalAlignment::to_json_string
- ::to_json_stringIntervalCoverage::to_json_string
T
KmerCount
- ::to_json_stringLocation::to_json_string
T
LocationSegment
- ::to_json_stringLocationSummary::to_json_string
- ::to_genbank_lineLocus::to_genbank_line
- ::to_json_stringLocus::to_json_string
- ::to_json_stringMotifHit::to_json_string
- ::to_json_stringMotifScanReport::to_json_string
- ::to_json_stringOpenReadingFrame::to_json_string
- ::to_genbank_linesQualifier::to_genbank_lines
- ::to_json_stringQualifierMatch::to_json_string
T
Range
- ::check_cds_translationsRecord::check_cds_translations
- ::features_by_keyRecord::features_by_key
- ::features_with_qualifierRecord::features_with_qualifier
- ::sequence_forRecord::sequence_for
- ::sequence_statsRecord::sequence_stats
- ::to_genbank_stringRecord::to_genbank_string
- ::to_json_stringRecord::to_json_string
- ::validateRecord::validate
- ::accessionsRecordCollection::accessions
- ::all_feature_keysRecordCollection::all_feature_keys
- ::atRecordCollection::at
- ::between_locationsRecordCollection::between_locations
- ::countRecordCollection::count
- ::definitionsRecordCollection::definitions
- ::feature_densityRecordCollection::feature_density
- ::filter_accessionRecordCollection::filter_accession
- ::filter_definitionRecordCollection::filter_definition
- ::filter_validRecordCollection::filter_valid
- ::fuzzy_locationsRecordCollection::fuzzy_locations
- ::gcRecordCollection::gc
- ::invalid_countRecordCollection::invalid_count
- ::map_normalizedRecordCollection::map_normalized
- ::recordsRecordCollection::records
- ::records_with_featureRecordCollection::records_with_feature
- ::remote_locationsRecordCollection::remote_locations
- ::reportsRecordCollection::reports
- ::sequence_signaturesRecordCollection::sequence_signatures
- ::source_nameRecordCollection::source_name
- ::summaryRecordCollection::summary
- ::to_fasta_stringRecordCollection::to_fasta_string
- ::to_genbank_stringRecordCollection::to_genbank_string
- ::total_basesRecordCollection::total_bases
- ::total_cdsRecordCollection::total_cds
- ::total_featuresRecordCollection::total_features
- ::total_genesRecordCollection::total_genes
- ::valid_countRecordCollection::valid_count
- ::validation_reportsRecordCollection::validation_reports
- ::to_json_stringRecordDiff::to_json_string
- ::to_textRecordDiff::to_text
- ::to_json_stringRecordMetrics::to_json_string
- ::to_textRecordMetrics::to_text
- ::to_json_stringSequenceAnalysis::to_json_string
T
SequenceInterval
- ::to_json_stringSequenceProfile::to_json_string
- ::to_json_stringSequenceQualityReport::to_json_string
- ::to_textSequenceRun::to_text
- ::to_json_stringSequenceStats::to_json_string
T
SequenceWindow
- ::to_json_stringTranslationAuditSummary::to_json_string
- ::to_tsvTranslationAuditSummary::to_tsv
T
TranslationCheck
- ::to_json_stringTranslationReport::to_json_string
- ::is_errorValidationIssue::is_error
- ::to_json_stringValidationIssue::to_json_string
- ::to_json_stringValidationReport::to_json_string
- ::to_textValidationReport::to_text
T
ValidationSeverity
V
align_sequences
V
aligned_iupac_consensus
V
alignment_display
V
alignment_operations
V
ambiguous_base_positions
V
ambiguous_codon_count
V
analyze_sequence
V
annotation_summary
V
assembly_contig_lengths
V
assembly_to_fasta
V
base_frequencies
V
base_profile
V
batch_checked_translation_count
V
batch_coding_bases
V
batch_failed_translation_count
V
batch_metric_invalid
V
batch_metric_max_length
V
batch_metric_mean_gc
V
batch_metric_mean_length
V
batch_metric_min_length
V
batch_metric_report
V
batch_metric_total_cds
V
batch_metric_total_features
V
batch_metric_total_genes
V
batch_metric_valid
V
batch_metrics
V
batch_metrics_json
V
batch_quality
V
batch_quality_from_text
V
batch_translation_audits
V
batch_translation_status
V
best_alignments
V
best_contig_overlap
V
build_feature_index
V
build_validation_report
V
cds_complete
V
cds_frame_length
V
cds_in_frame
V
cds_nucleotide_lengths
V
cds_partial
V
cds_protein_lengths
V
cds_start_codons
V
cds_terminal_codons
V
cds_translation_error_count
V
cds_translation_json
V
cds_translation_matches
V
cds_translation_mismatches
V
cds_translation_ok
V
cds_translation_results
V
cds_translation_summary
V
cds_with_start_codon
V
cds_with_stop_codon
V
change_points
V
clean_records
V
coding_sequence_report
V
codon_amino
V
codon_frequency_by_amino
V
codon_usage
V
codon_usage_frequencies
V
codon_usage_ranked
V
codon_usage_total
V
collection_fasta
V
collection_from_records
V
collection_json
V
common_dna_motifs
V
compare_records
V
composition_report
V
consensus_sequence
V
coordinate_coverage
V
coordinate_mask
V
count_base
V
count_not_in
V
distinct_codon_count
V
dna_sequence
V
extract_cds
V
extract_features
V
failed_translation_checks_tsv
V
fasta_length_histogram
V
feature_at_coordinate
V
feature_coverage
V
feature_coverage_percent
V
feature_density
V
feature_end
V
feature_extractions_json
V
feature_gene_name
V
feature_has_fuzzy_location
V
feature_has_remote_location
V
feature_has_translation
V
feature_is_cds
V
feature_is_empty
V
feature_is_gene
V
feature_is_source
V
feature_key_counts
V
feature_key_coverage
V
feature_key_summary
V
feature_key_summary_tsv
V
feature_length
V
feature_note_values
V
feature_overlaps_any
V
feature_product_name
V
feature_qualifier_count
V
feature_qualifier_counts
V
feature_qualifier_names
V
feature_qualifier_values
V
feature_search
V
feature_sequence_lengths
V
feature_signatures
V
feature_span
V
feature_start
V
feature_summary_text
V
feature_table
V
feature_table_by_key
V
feature_table_row
V
feature_table_tsv
V
features_in_length_range
V
features_with_location_property
V
features_with_qualifier_text
V
features_with_strand
V
find_motif_positions
V
find_orfs
V
find_qualifier_matches
V
find_qualifier_value_matches
V
first_feature_by_key
V
format_fasta_records
V
gap_count
V
gc_profile
V
gc_skew_profile
V
gc_skew_windows
V
genbank_round_trip
V
gene_summary_json
V
global_align
V
greedy_assemble
V
hamming_distance
V
has_motif
V
highest_gc_profile
V
homopolymer_runs
V
intersect_coordinate_intervals
V
interval_contains
V
interval_coverage
V
intervals_to_text
V
invalid_base_positions
V
is_iupac_base
V
is_palindromic_motif
V
is_valid_dna
V
iupac_consensus
V
iupac_expansion
V
iupac_motif_count
V
iupac_motif_matches_at
V
iupac_motif_positions
V
join_sequences
V
kmer_profile
V
local_features_fit_origin
V
location_between_ranges
V
location_contains
V
location_coordinates
V
location_distance
V
location_forward_coordinates
V
location_has_overlap
V
location_intervals
V
location_is_complemented
V
location_is_fuzzy
V
location_is_joined
V
location_is_ordered
V
location_is_remote
V
location_is_single_range
V
location_length
V
location_minimum
V
location_overlap_length
V
location_partial_ranges
V
location_range_text
V
location_ranges_text
V
location_remote_accessions
V
location_segments
V
location_span
V
location_summary_text
V
location_unique_coordinates
V
longest_fasta_record
V
longest_homopolymer
V
longest_sequence_run
V
longest_translation
V
mask_ambiguities
V
mask_ambiguous
V
mask_to_intervals
V
merge_coordinate_intervals
V
metric_between_count
V
metric_cds_count
V
metric_coverage
V
metric_coverage_percent
V
metric_entropy
V
metric_error_count
V
metric_feature_count
V
metric_fuzzy_count
V
metric_gc
V
metric_gene_count
V
metric_length
V
metric_remote_count
V
metric_warning_count
V
most_ambiguous_profile
V
motif_count
V
motif_density
V
normalize_genbank_text
V
normalize_record
V
normalize_sequence
V
normalize_spaces
V
nucleotide_length
V
pad_sequence
V
parse_fasta
V
parse_fasta_strict
V
parse_location
V
parse_locus
V
parse_record
V
parse_record_collection
V
parse_records
V
profile_has_ambiguity
V
profile_mean_gc
V
profile_total_motif_hits
V
profile_window_count
V
project_feature
V
project_interval
V
project_record_features
V
protein_has_unknowns
V
protein_is_empty
V
protein_length
V
protein_molecular_weight_approximation
V
protein_stop_count
V
protein_unknown_count
V
qualifier_difference
V
qualifier_exists
V
qualifier_histogram
V
qualifier_match_json
V
qualifier_match_text
V
qualifier_name_count
V
qualifier_names_for_record
V
qualifier_search
V
qualifier_value
V
qualifier_value_count
V
qualifier_value_exists
V
qualifier_values_for_feature
V
qualifier_values_json
V
record_annotation_report
V
record_between_location_count
V
record_cds_count
V
record_coding_reports
V
record_complete_codon_count
V
record_error_count
V
record_feature_labels
V
record_feature_report
V
record_feature_span
V
record_fuzzy_location_count
V
record_gene_count
V
record_gene_names
V
record_has_terminator
V
record_has_translation_errors
V
record_is_normalized
V
record_is_valid
V
record_key_coverage
V
record_location_json
V
record_location_summaries
V
record_locus_tags
V
record_maximum_feature_end
V
record_metrics
V
record_metrics_json
V
record_metrics_text
V
record_minimum_feature_start
V
record_notes
V
record_organisms
V
record_origin_chunks
V
record_products
V
record_qualifier_report
V
record_references
V
record_remote_accession_count
V
record_report
V
record_report_json
V
record_source_count
V
record_span
V
record_text_length
V
record_text_lines
V
record_to_bed
V
record_to_fasta
V
record_to_gff3
V
record_translations
V
record_warning_count
V
records_equivalent
V
records_with_consistent_translations
V
remove_gaps
V
render_location
V
reverse_complement
V
reverse_complement_frames
V
rna_sequence
V
scan_iupac_both_strands
V
scan_iupac_motif
V
sequence_chunks
V
sequence_complexity
V
sequence_edit_distance
V
sequence_entropy_profile
V
sequence_gc_skew
V
sequence_identity
V
sequence_is_clean
V
sequence_is_low_complexity
V
sequence_pairwise_identity
V
sequence_palindrome
V
sequence_profile
V
sequence_profiles_tsv
V
sequence_quality_flags
V
sequence_quality_ok
V
sequence_quality_report
V
sequence_runs
V
sequence_signature
V
sequence_subsequence
V
sequence_windows
V
shortest_translation
V
sort_fasta_by_length
V
sorted_feature_keys
V
sorted_qualifier_names
V
source_feature
V
standard_codon_table
V
stop_codon_count
V
stop_codon_fraction
V
suffix_prefix_overlap
V
summarize_alignment
V
summarize_location
V
summarize_records
V
synonymous_codon_count
V
translate_all_frames
V
translate_dna
V
translate_dna_report
V
translate_feature
V
translate_frame
V
translation_audit
V
translation_checks_json
V
translation_has_internal_stop
V
translation_is_terminated
V
translation_lengths
V
translation_pass_rate
V
translation_without_stop
V
translations_are_consistent
V
trim_sequence
V
ungapped_intervals
V
unresolved_feature_count
V
validate_fasta_records
V
validate_fasta_text
V
vertebrate_mitochondrial_table