List of all items

Structs

• alignment::scoring::ScoringMatrix
• alignment::smith_waterman::Alignment
• formats::bed::Bed12Record
• formats::bed::Bed3Record
• formats::bed::Bed6Record
• formats::bed::NarrowPeakRecord
• formats::gfa::GfaHeader
• formats::gfa::GfaLink
• formats::gfa::GfaParser
• formats::gfa::GfaPath
• formats::gfa::GfaSegment
• formats::gff::Gff3Parser
• formats::gff::Gff3Record
• formats::gtf::GtfParser
• formats::gtf::GtfRecord
• formats::index::tbi::TbiBin
• formats::index::tbi::TbiIndex
• formats::index::tbi::TbiReference
• formats::paf::PafParser
• formats::paf::PafRecord
• formats::primitives::genomic::GenomicInterval
• formats::primitives::header::HeaderParser
• formats::primitives::tab_delimited::TabDelimitedParser
• formats::vcf::VcfHeader
• formats::vcf::VcfParser
• formats::vcf::VcfRecord
• io::FastqStream
• io::FastqWriter
• io::PairedFastqStream
• io::bam::header::Header
• io::bam::header::Reference
• io::bam::index::BaiIndex
• io::bam::index::Bin
• io::bam::index::Chunk
• io::bam::index::ReferenceIndex
• io::bam::index::VirtualOffset
• io::bam::reader::BamReader
• io::bam::reader::Records
• io::bam::reader::RegionQuery
• io::bam::record::Record
• io::bam::sam_writer::SamWriter
• io::bam::tags::Tag
• io::bam::tags::Tags
• io::compression::CompressedReader
• io::compression::SeekableBgzfReader
• io::fasta::FastaStream
• io::fasta::index::FaiEntry
• io::fasta::index::FaiIndex
• io::network::CacheStats
• io::network::HttpClient
• io::network::HttpReader
• operations::kmer::KmerExtractor
• operations::kmer::Minimizer
• operations::nthash::NtHashForwardIterator
• operations::nthash::NtHashIterator
• operations::sliding_min::MinElem
• operations::sliding_min::SlidingMin
• types::FastaRecord
• types::FastqRecord

Enums

• alignment::cigar::CigarOp
• error::BiometalError
• formats::gfa::GfaRecord
• formats::gfa::Orientation
• formats::index::tbi::TbiFormat
• formats::primitives::FormatError
• formats::primitives::genomic::Strand
• io::bam::cigar::CigarOp
• io::bam::error::BamDecodeError
• io::bam::tags::ArrayValue
• io::bam::tags::TagValue
• io::compression::CompressedWriter
• io::compression::DataSource
• io::sink::DataSink
• optimization::Platform

Traits

• formats::primitives::tab_delimited::TabDelimitedRecord

Functions

• alignment::cigar::compress_cigar
• alignment::cigar::format_cigar
• alignment::smith_waterman::smith_waterman
• alignment::smith_waterman::smith_waterman_naive
• formats::primitives::fields::parse_attributes
• formats::primitives::fields::parse_comma_list
• formats::primitives::fields::parse_optional
• formats::primitives::fields::parse_required
• formats::primitives::fields::split_fields
• io::bam::cigar::parse_cigar
• io::bam::header::read_header
• io::bam::header::read_header_text
• io::bam::header::read_magic
• io::bam::header::read_reference
• io::bam::header::read_references
• io::bam::record::parse_record
• io::bam::record::read_record
• io::bam::sequence::decode_sequence
• io::bam::tags::parse_tags
• io::compression::decompress_bgzip_parallel
• io::sra::is_sra_accession
• io::sra::sra_to_url
• operations::base_counting::count_bases
• operations::base_counting::count_bases_scalar
• operations::block::count_bases_block
• operations::block::count_bases_block_scalar
• operations::block::gc_content_block
• operations::block::gc_content_block_scalar
• operations::block::mean_quality_block
• operations::block::mean_quality_block_scalar
• operations::complexity::complexity_score
• operations::complexity::complexity_score_scalar
• operations::gc_content::gc_content
• operations::gc_content::gc_content_scalar
• operations::kmer::extract_kmers
• operations::kmer::extract_minimizers
• operations::kmer::extract_minimizers_fast
• operations::kmer::kmer_iter
• operations::kmer::kmer_spectrum
• operations::masking::count_masked_bases
• operations::masking::mask_low_quality
• operations::masking::mask_low_quality_copy
• operations::quality_filter::mean_quality
• operations::quality_filter::mean_quality_scalar
• operations::quality_filter::passes_quality_filter
• operations::record_ops::extract_region
• operations::record_ops::meets_length_requirement
• operations::record_ops::reverse_complement_record
• operations::record_ops::reverse_complement_record_inplace
• operations::record_ops::sequence_length
• operations::record_ops::to_fasta_record
• operations::sequence::complement
• operations::sequence::complement_inplace
• operations::sequence::count_invalid_bases
• operations::sequence::is_valid_dna
• operations::sequence::is_valid_rna
• operations::sequence::reverse
• operations::sequence::reverse_complement
• operations::sequence::reverse_complement_inplace
• operations::sequence::reverse_inplace
• operations::sliding_min::sliding_min_iter
• operations::trimming::trim_both
• operations::trimming::trim_end
• operations::trimming::trim_quality_both
• operations::trimming::trim_quality_end
• operations::trimming::trim_quality_start
• operations::trimming::trim_quality_window
• operations::trimming::trim_start
• optimization::has_neon

Type Aliases

• error::Result
• formats::primitives::Result
• operations::base_counting::BaseCounts
• operations::gc_content::GCContent

Constants

• VERSION
• io::compression::MMAP_THRESHOLD
• io::network::DEFAULT_CACHE_SIZE
• io::network::DEFAULT_MAX_RETRIES
• io::network::DEFAULT_PREFETCH_COUNT
• io::network::DEFAULT_PREFETCH_WORKERS
• io::network::DEFAULT_TIMEOUT
• io::network::MAX_CACHE_SIZE
• io::network::MIN_CACHE_SIZE
• operations::nthash::MAX_K_SIZE
• optimization::BLOCK_SIZE
• optimization::MMAP_THRESHOLD