List of all items

Structs

• convert::command::BioinformaticsFilePair
• convert::command::ConvertArgs
• derive::command::DeriveArgs
• derive::command::instrument::DeriveInstrumentArgs
• derive::instrument::compute::DerivedInstrumentResult
• derive::instrument::compute::InstrumentDetectionResults
• derive::instrument::reads::IlluminaReadName
• generate::command::GenerateArgs
• generate::providers::reference_provider::ReferenceGenomeSequenceProvider
• generate::utils::NormalDistributionParams
• generate::utils::PairedRead
• generate::utils::SeqLen
• index::command::IndexArgs
• list::command::ListArgs
• plot::cohort::PlotCohortArgs
• plot::cohort::gc_content_distribution::GCContentDistributionPlot
• plot::command::FilepathResults
• plot::command::PlotArgs
• plot::sample::PlotSampleArgs
• plot::sample::gc_content_distribution::GCContentDistributionPlot
• plot::sample::quality_score_distribution::QualityScoreDistributionPlot
• plot::sample::vaf_distribution::VariantAlleleFractionDistributionPlot
• qc::command::QcArgs
• qc::record_based::features::FeatureNames
• qc::record_based::features::GenomicFeaturesFacet
• qc::record_based::features::metrics::ExonicTranslationRegionMetrics
• qc::record_based::features::metrics::GeneRegionMetrics
• qc::record_based::features::metrics::Metrics
• qc::record_based::features::metrics::RecordMetrics
• qc::record_based::features::metrics::SummaryMetrics
• qc::record_based::features::utils::FeatureNameStrand
• qc::record_based::features::utils::StrandParseError
• qc::record_based::gc_content::GCContentFacet
• qc::record_based::gc_content::metrics::GCContentMetrics
• qc::record_based::gc_content::metrics::NucleobaseMetrics
• qc::record_based::gc_content::metrics::RecordMetrics
• qc::record_based::gc_content::metrics::SummaryMetrics
• qc::record_based::general::GeneralMetricsFacet
• qc::record_based::general::metrics::CigarMetrics
• qc::record_based::general::metrics::GeneralMetrics
• qc::record_based::general::metrics::ReadDesignationMetrics
• qc::record_based::general::metrics::RecordMetrics
• qc::record_based::general::metrics::SummaryMetrics
• qc::record_based::quality_scores::QualityScoreFacet
• qc::record_based::template_length::RecordMetrics
• qc::record_based::template_length::SummaryMetrics
• qc::record_based::template_length::TemplateLengthFacet
• qc::results::Results
• qc::sequence_based::coverage::CoverageFacet
• qc::sequence_based::coverage::CoverageMetrics
• qc::sequence_based::coverage::IgnoredMetrics
• qc::sequence_based::edits::EditMetrics
• qc::sequence_based::edits::EditMetricsSummary
• qc::sequence_based::edits::EditsFacet
• utils::alignment::ReferenceRecordStepThrough
• utils::display::PercentageFormat
• utils::display::RecordCounter
• utils::formats::bam::ParsedAsyncBAMFile
• utils::formats::bam::ParsedBAMFile
• utils::formats::cram::ParsedAsyncCRAMFile
• utils::formats::cram::ParsedCRAMFile
• utils::formats::sam::ParsedAsyncSAMFile
• utils::formats::sam::ParsedSAMFile
• utils::formats::utils::RawAndParsedHeaders
• utils::genome::Sequence
• utils::genome::ncbi::grch38_no_alt::GRCh38NoAltAnalysisSet
• utils::histogram::BinOutOfBoundsError
• utils::histogram::Histogram
• view::command::ViewArgs

Enums

• derive::command::DeriveSubcommand
• plot::command::PlotSubcommand
• qc::ComputationalLoad
• qc::record_based::features::utils::Strand
• utils::args::CompressionStrategy
• utils::args::NumberOfRecords
• utils::formats::BioinformaticsFileError
• utils::formats::BioinformaticsFileFormat
• utils::formats::utils::IndexCheck
• utils::genome::GenomeBasis
• utils::genome::SequenceKind
• view::command::Mode

Traits

• generate::providers::SequenceProvider
• plot::command::CohortPlot
• plot::command::SamplePlot
• qc::RecordBasedQualityControlFacet
• qc::SequenceBasedQualityControlFacet
• utils::genome::ReferenceGenome
• utils::pathbuf::AppendExtension

Macros

• sequence

Functions

• convert::bam::to_cram_async
• convert::bam::to_sam_async
• convert::command::convert
• convert::cram::to_bam_async
• convert::cram::to_sam_async
• convert::gff::to_block_gzipped_gff
• convert::sam::to_bam_async
• convert::sam::to_cram_async
• derive::command::instrument::derive
• derive::instrument::compute::possible_instruments_for_query
• derive::instrument::compute::predict
• derive::instrument::compute::predict_instrument
• derive::instrument::compute::resolve_instrument_prediction
• derive::instrument::flowcells::build_flowcell_lookup_table
• derive::instrument::instruments::build_instrument_lookup_table
• generate::command::error_rate_in_range
• generate::command::generate
• generate::providers::simulate_errors
• generate::utils::compliment
• generate::utils::reverse_compliment
• index::bam::index
• index::command::index
• index::cram::index
• index::fasta::index
• list::command::list
• plot::cohort::plot
• plot::command::get_all_cohort_plots
• plot::command::get_all_sample_plots
• plot::sample::plot
• qc::command::qc
• qc::get_qc_facets
• utils::alignment::flatten
• utils::cigar::consumes_reference
• utils::cigar::consumes_sequence
• utils::formats::bam::open_and_parse
• utils::formats::bam::open_and_parse_async
• utils::formats::cram::open_and_parse
• utils::formats::cram::open_and_parse_async
• utils::formats::fasta::open
• utils::formats::fastq::writer
• utils::formats::gff::open
• utils::formats::sam::correct_common_header_mistakes
• utils::formats::sam::open_and_parse
• utils::formats::sam::open_and_parse_async
• utils::formats::sam::parse_header
• utils::genome::get_all_reference_genomes
• utils::genome::get_all_sequences
• utils::genome::get_primary_assembly
• utils::genome::get_reference_genome
• view::bam::view
• view::command::view
• view::cram::view
• view::gff::view
• view::sam::view

Constants

• qc::record_based::gc_content::TRUNCATION_LENGTH
• qc::record_based::quality_scores::MAX_SCORE