List of all items
Structs
- bed::PaddedIntervalSampler
- bed::TargetRegions
- commands::common::BedOptions
- commands::common::OutputPrefixOptions
- commands::common::ReferenceOptions
- commands::common::SeedOptions
- commands::common::VcfOptions
- commands::eval::Eval
- commands::methylate::Methylate
- commands::mutate::Mutate
- commands::simulate::Simulate
- error_model::illumina::IlluminaErrorModel
- fasta::Fasta
- fragment::Fragment
- haplotype::Haplotype
- haplotype::HaplotypeVariant
- meth::ContigMethylation
- meth::MethylationAnnotation
- meth::MethylationConfig
- meth::MethylationRecordTags
- meth::MethylationTable
- methylation_tags::CallTags
- output::cpg_truth::CpgTruthTally
- output::fastq::FastqWriter
- output::golden_bam::GoldenBamMetadata
- output::golden_bam::GoldenBamWriter
- ploidy::PloidyMap
- read::ReadPair
- read::SimulatedRead
- read_naming::TruthAlignment
- sequence_dict::SequenceDictionary
- sequence_dict::SequenceMetadata
- vcf::ParsedVariants
- vcf::genotype::Genotype
- vcf::genotype::VariantRecord
- vcf::methylation::MethylationVcfRecords
Enums
- error_model::ReadEnd
- meth::ConversionType
- meth::MethylationMode
- vcf::methylation::ClassifyError
- vcf::methylation::CpgPlacement
- vcf::methylation::ReadError
Traits
Functions
- commands::command::output_path
- error_model::apply_errors
- fragment::extract_fragment
- fragment::extract_read_bases
- fragment::lowercase_fraction
- fragment::reverse_complement
- fragment::uppercase_in_place
- haplotype::build_haplotypes
- meth::apply_methylation_conversion
- methylation_tags::compute_call_tags
- methylation_tags::populate_pair_call_tags
- output::methylation_bedgraph::write_bedgraph
- output::methylation_bedgraph::write_bedgraph_header
- output::methylation_bedgraph::write_bedgraph_records
- read::cigar_from_ref_positions
- read::cigar_to_string
- read::generate_read_pair
- read_naming::encoded_pe_name
- read_naming::encoded_se_name
- read_naming::parse_encoded_pe_name
- read_naming::parse_encoded_se_name
- read_naming::simple_name
- seed::compute_seed
- seed::derive_seed
- seed::resolve_seed
- vcf::methylation::classify_cpgs
- vcf::methylation::load_contig_methylation_from_records
- vcf::methylation::parse_methylation_vcf
- vcf::methylation::read_contig_methylation
- vcf::methylation::vcf_has_mt_mb_records
- vcf::methylation::write_contig
- vcf::methylation::write_vcf_header
- vcf::parse_variants_by_contig
Statics
- version::CFG_ENDIAN
- version::CFG_ENV
- version::CFG_FAMILY
- version::CFG_OS
- version::CFG_POINTER_WIDTH
- version::CFG_TARGET_ARCH
- version::CI_PLATFORM
- version::DEBUG
- version::FEATURES
- version::FEATURES_LOWERCASE
- version::FEATURES_LOWERCASE_STR
- version::FEATURES_STR
- version::GIT_COMMIT_HASH
- version::GIT_COMMIT_HASH_SHORT
- version::GIT_DIRTY
- version::GIT_HEAD_REF
- version::GIT_VERSION
- version::HOST
- version::NUM_JOBS
- version::OPT_LEVEL
- version::OVERRIDE_VARIABLES_USED
- version::PKG_AUTHORS
- version::PKG_DESCRIPTION
- version::PKG_HOMEPAGE
- version::PKG_LICENSE
- version::PKG_NAME
- version::PKG_REPOSITORY
- version::PKG_VERSION
- version::PKG_VERSION_MAJOR
- version::PKG_VERSION_MINOR
- version::PKG_VERSION_PATCH
- version::PKG_VERSION_PRE
- version::PROFILE
- version::RUSTC
- version::RUSTC_VERSION
- version::RUSTDOC
- version::RUSTDOC_VERSION
- version::TARGET
- version::VERSION