wju-yuki111/moonbit-gffkit/cmd/gffkit

README
- ::attribute_frequenciesAnnotation::attribute_frequencies
- ::attribute_frequency_tsvAnnotation::attribute_frequency_tsv
- ::build_interval_indexAnnotation::build_interval_index
- ::coding_featuresAnnotation::coding_features
- ::count_by_typeAnnotation::count_by_type
- ::exon_featuresAnnotation::exon_features
- ::feature_table_tsvAnnotation::feature_table_tsv
- ::features_by_classAnnotation::features_by_class
- ::filter_by_typeAnnotation::filter_by_type
- ::find_by_attributeAnnotation::find_by_attribute
- ::gene_featuresAnnotation::gene_features
- ::gene_metrics_tsvAnnotation::gene_metrics_tsv
- ::gene_table_tsvAnnotation::gene_table_tsv
- ::infer_attribute_schemaAnnotation::infer_attribute_schema
- ::metricsAnnotation::metrics
- ::overlappingAnnotation::overlapping
- ::quality_reportAnnotation::quality_report
- ::sequence_summariesAnnotation::sequence_summaries
- ::sequence_summary_tsvAnnotation::sequence_summary_tsv
- ::summaryAnnotation::summary
- ::to_bedAnnotation::to_bed
- ::to_bed12Annotation::to_bed12
- ::to_gene_modelsAnnotation::to_gene_models
- ::to_gff3Annotation::to_gff3
- ::to_gtfAnnotation::to_gtf
- ::to_jsonAnnotation::to_json
- ::transcript_featuresAnnotation::transcript_features
- ::transcript_metrics_tsvAnnotation::transcript_metrics_tsv
- ::transcript_table_tsvAnnotation::transcript_table_tsv
- ::type_reportAnnotation::type_report
- ::type_report_tsvAnnotation::type_report_tsv
- ::unknown_reference_termsAnnotation::unknown_reference_terms
- ::utr_featuresAnnotation::utr_features
- ::validateAnnotation::validate
- ::is_emptyAnnotationMetrics::is_empty
- ::mean_feature_lengthAnnotationMetrics::mean_feature_length
- ::to_textAnnotationMetrics::to_text
T
Attribute
- ::to_tsv_rowAttributeFrequency::to_tsv_row
- ::to_stringAttributePresence::to_string
- ::to_tsv_rowAttributeReference::to_tsv_row
- ::optional_keysAttributeSchema::optional_keys
- ::rare_keysAttributeSchema::rare_keys
- ::required_keysAttributeSchema::required_keys
- ::to_tsvAttributeSchema::to_tsv
T
AttributeSchemaRow
- ::to_lineBed12Record::to_line
- ::to_tsv_rowBiotypeReference::to_tsv_row
T
Diagnostic
- ::to_tsv_rowEvidenceReference::to_tsv_row
- ::attributeFeature::attribute
- ::bed_startFeature::bed_start
- ::display_nameFeature::display_name
- ::feature_classFeature::feature_class
- ::has_parentFeature::has_parent
- ::is_coding_featureFeature::is_coding_feature
- ::is_exon_featureFeature::is_exon_feature
- ::is_gene_featureFeature::is_gene_feature
- ::is_regulatory_featureFeature::is_regulatory_feature
- ::is_repeat_featureFeature::is_repeat_feature
- ::is_transcript_feature_publicFeature::is_transcript_feature_public
- ::is_utr_featureFeature::is_utr_feature
- ::lengthFeature::length
- ::overlapsFeature::overlaps
- ::reference_termFeature::reference_term
- ::region_stringFeature::region_string
- ::spanFeature::span
- ::stable_idFeature::stable_id
- ::to_bed_lineFeature::to_bed_line
- ::to_debug_tsvFeature::to_debug_tsv
- ::to_gff3_lineFeature::to_gff3_line
- ::to_gtf_lineFeature::to_gtf_line
- ::to_half_open_endFeature::to_half_open_end
- ::to_zero_based_startFeature::to_zero_based_start
- ::to_stringFeatureClass::to_string
T
FeatureCount
- ::to_tsv_rowFeatureTermReference::to_tsv_row
- ::to_stringFormat::to_string
- ::is_multi_transcriptGeneMetrics::is_multi_transcript
- ::to_tsv_rowGeneMetrics::to_tsv_row
- ::metricsGeneModel::metrics
T
IntervalHit
- ::count_seqidIntervalIndex::count_seqid
- ::features_onIntervalIndex::features_on
- ::queryIntervalIndex::query
- ::query_spanIntervalIndex::query_span
- ::seqidsIntervalIndex::seqids
- ::gradeQualityReport::grade
- ::to_textQualityReport::to_text
T
ReferenceTerm
- ::to_tsv_rowSequenceRegionReference::to_tsv_row
- ::span_basesSequenceSummary::span_bases
- ::to_tsv_rowSequenceSummary::to_tsv_row
- ::to_stringSeverity::to_string
- ::containsSpan::contains
- ::distance_toSpan::distance_to
- ::expandSpan::expand
- ::lengthSpan::length
- ::overlap_lengthSpan::overlap_length
- ::overlapsSpan::overlaps
- ::shiftSpan::shift
- ::to_bed_endSpan::to_bed_end
- ::to_bed_startSpan::to_bed_start
- ::to_region_stringSpan::to_region_string
- ::to_stringStrand::to_string
T
Summary
- ::coding_ratioTranscriptMetrics::coding_ratio
- ::has_cdsTranscriptMetrics::has_cds
- ::has_intronsTranscriptMetrics::has_introns
- ::to_tsv_rowTranscriptMetrics::to_tsv_row
- ::metricsTranscriptModel::metrics
- ::to_bed12TranscriptModel::to_bed12
- ::to_tsv_rowTypeReportRow::to_tsv_row
- ::is_errorValidationIssue::is_error
- ::is_infoValidationIssue::is_info
- ::is_warningValidationIssue::is_warning
- ::rule_referenceValidationIssue::rule_reference
- ::summaryValidationIssue::summary
- ::codesValidationReport::codes
- ::count_by_severityValidationReport::count_by_severity
- ::error_countValidationReport::error_count
- ::filter_by_codeValidationReport::filter_by_code
- ::filter_by_feature_typeValidationReport::filter_by_feature_type
- ::has_errorsValidationReport::has_errors
- ::info_countValidationReport::info_count
- ::issue_countValidationReport::issue_count
- ::summary_tsvValidationReport::summary_tsv
- ::to_textValidationReport::to_text
- ::warning_countValidationReport::warning_count
- ::to_tsv_rowValidationRuleReference::to_tsv_row
V
coding_reference_biotypes
V
evidence_references
V
evidence_references_by_category
V
evidence_references_by_source
V
example_complex_gff3
V
example_complex_gtf
V
feature_term_references
V
feature_term_references_by_category
V
find_evidence_reference
V
find_feature_term_reference
V
find_reference_attribute
V
find_reference_biotype
V
find_reference_term
V
find_sequence_region_reference
V
find_validation_rule_reference
V
noncoding_reference_biotypes
V
parse_auto
V
parse_gff3
V
parse_gtf
V
reference_attributes
V
reference_attributes_by_category
V
reference_attributes_by_format
V
reference_attributes_tsv
V
reference_biotypes
V
reference_biotypes_by_family
V
reference_term_categories
V
reference_terms
V
reference_terms_by_category
V
sequence_region_references
V
sequence_region_references_by_category
V
sequence_region_references_by_topology
V
validation_rule_references
V
validation_rule_references_by_format