List of all items

Structs

• barcode::atrandi_rnaseq_barcode::AtrandiRNAseqChemistry
• barcode::atrandi_wgs_barcode::AtrandiWGSChemistry
• barcode::combinatorial_barcode::CombinatorialBarcode
• barcode::combinatorial_barcode::CombinatorialBarcodePart
• barcode::combinatorial_barcode::MyersBarcode
• barcode::general_barcode::GeneralCombinatorialBarcode
• barcode::petriseq_barcode::PetriseqChemistry
• barcode::tenx::tenx::TenxChemistry
• command::bam2fragments::Bam2Fragments
• command::bam2fragments::Bam2FragmentsCMD
• command::countchrom::CountChrom
• command::countchrom::CountChromCMD
• command::countchrom::SparseCountMatrix
• command::countfeature::CellCounter
• command::countfeature::ChromosomeCounter
• command::countfeature::CountFeature
• command::countfeature::CountFeatureCMD
• command::countfeature::GeneCounter
• command::countfeature::GenomeCounter
• command::countsketch_mat::CountsketchCMD
• command::countsketch_mat::CountsketchMat
• command::extract::ExtractCMD
• command::extract_terminal::ExtractStream
• command::extract_terminal::ExtractStreamCMD
• command::featurise_kmc::FeaturiseKMC
• command::featurise_kmc::FeaturiseKmcCMD
• command::featurise_kmc::FeaturiseParamsKMC
• command::getraw::GetRaw
• command::getraw::GetRawCMD
• command::getraw::RecordPair
• command::kraken::Kraken
• command::kraken::KrakenCMD
• command::kraken::KrakenCountMatrix
• command::mapcell::MapCell
• command::mapcell::MapCellCMD
• command::minhash_hist::MinhashHist
• command::minhash_hist::MinhashHistCMD
• command::query_fq::QueryFq
• command::query_fq::QueryFqCMD
• command::query_kmc::QueryKmc
• command::query_kmc::QueryKmcCMD
• command::query_kmc::QueryKmcParams
• command::sam_add_barcode_tag_cmd::PipeSamAddTagsCMD
• command::shardify::Shardify
• command::shardify::ShardifyCMD
• command::transform::TransformCMD
• command::transform::TransformFile
• fileformat::bam::BAMStreamingReadPairReader
• fileformat::bam::BAMStreamingReadPairReaderFactory
• fileformat::count_matrix::SparseCountMatrix
• fileformat::list_fastq::ListFastqReader
• fileformat::list_fastq::ListFastqReaderFactory
• fileformat::paired_fastq::BascetPairedFastqWriter
• fileformat::paired_fastq::BascetPairedFastqWriterFactory
• fileformat::paired_fastq::PairedFastqStreamingReadPairReader
• fileformat::paired_fastq::PairedFastqStreamingReadPairReaderFactory
• fileformat::shard::BarcodeHistogram
• fileformat::shard::ReadPair
• fileformat::single_fastq::BascetSingleFastqWriter
• fileformat::single_fastq::BascetSingleFastqWriterFactory
• fileformat::tirp::BascetTIRPWriter
• fileformat::tirp::BascetTIRPWriterFactory
• fileformat::tirp::TirpBascetShardReader
• fileformat::tirp::TirpBascetShardReaderFactory
• fileformat::tirp::TirpStreamingReadPairReader
• fileformat::tirp::TirpStreamingReadPairReaderFactory
• fileformat::tirp::TirpStreamingShardExtractor
• fileformat::tirp::TirpStreamingShardReaderFactory
• fileformat::zip::ZipBascetShardReader
• fileformat::zip::ZipBascetShardReaderFactory
• kmer::bounded_heap::BoundedMinHeap
• kmer::kmc_counter::CountSketch
• kmer::kmc_counter::KmerCounter
• kmer::kmer_codec::KMERCodec
• kmer::kmer_codec::KMERandCount
• mapcell::mapcell_script::MapCellFunctionShellScript
• mapcell_scripts::countsketch_fq::MapCellCountSketchFQ
• mapcell_scripts::minhash_fq::MapCellMinHashFQ
• mapcell_scripts::minhash_kmc::MapCellMinHashKMC

Enums

• fileformat::DetectedFileformat
• fileformat::shard::DynShardReader
• kmer::bounded_heap::HeapError
• mapcell::mapcell_function::CompressionMode
• mapcell::mapcell_function::MissingFileMode

Traits

• barcode::chemistry::Chemistry
• fileformat::shard::ConstructFromPath
• fileformat::shard::ReadPairReader
• fileformat::shard::ReadPairWriter
• fileformat::shard::ShardCellDictionary
• fileformat::shard::ShardRandomFileExtractor
• fileformat::shard::ShardStreamingFileExtractor
• fileformat::shard::StreamingReadPairReader
• kmer::bounded_heap::BoundedHeap
• mapcell::mapcell_function::MapCellFunction

Functions

• barcode::atrandi_wgs_barcode::find_subsequence
• barcode::trim_pairwise::revcomp
• barcode::trim_pairwise::revcomp_n
• command::bam2fragments::index_fragments
• command::featurise_kmc::dump_kmc_db
• command::getraw::catsort_files
• command::getraw::loop_tirp_writer
• command::getraw::open_fastq
• command::getraw::sum_and_store_histogram
• command::query_kmc::count_from_dump
• command::threadcount::determine_thread_counts_1
• command::threadcount::determine_thread_counts_2
• command::threadcount::determine_thread_counts_3
• command::threadcount::determine_thread_counts_mapcell
• command::threadcount::min1
• command::threadcount::some_min1
• command::transform::create_random_readers
• command::transform::create_stream_reader_thread
• command::transform::create_stream_readers
• fileformat::bam::readname_to_cell_umi
• fileformat::cell_list_file::read_cell_list_file
• fileformat::detect_shard_format
• fileformat::get_suitable_file_extractor
• fileformat::list_fastq::open_fastq
• fileformat::shard::get_dyn_celldict
• fileformat::shard::get_shard_reader_for_path
• fileformat::shard::try_get_cells_in_file
• fileformat::tirp::get_histogram_path_for_tirp
• fileformat::tirp::get_tbi_path_for_tirp
• fileformat::tirp::index_tirp
• fileformat::tirp::parse_tirp_readpair
• fileformat::tirp::parse_tirp_readpair_with_cellid
• fileformat::tirp::write_records_pair_to_tirp
• fileformat::uuencode::convert_from_uuencode
• fileformat::uuencode::convert_to_uuencode
• fileformat::verify_input_fq_file
• mapcell::mapcell_function::parse_compression_mode
• mapcell::mapcell_function::parse_missing_file_mode
• mapcell::mapcell_script::get_script_expect_files
• mapcell::mapcell_script::to_absolute_path
• mapcell_scripts::mapcell_scripts::get_preset_script
• mapcell_scripts::mapcell_scripts::get_preset_script_names
• playground::mapshard::test
• utils::check_bgzip
• utils::check_kmc_tools
• utils::check_samtools
• utils::check_tabix
• utils::dedup_umi
• utils::merge_archives
• utils::merge_archives_and_delete

Type Aliases

• fileformat::shard::CellID
• fileformat::shard::CellUMI

Constants

• command::bam2fragments::DEFAULT_PATH_TEMP
• command::bam2fragments::DEFAULT_THREADS
• command::countchrom::DEFAULT_PATH_TEMP
• command::countsketch_mat::DEFAULT_PATH_TEMP
• command::countsketch_mat::DEFAULT_THREADS_READ
• command::countsketch_mat::DEFAULT_THREADS_WORK
• command::countsketch_mat::DEFAULT_THREADS_WRITE
• command::extract::DEFAULT_PATH_TEMP
• command::extract_terminal::DEFAULT_PATH_TEMP
• command::featurise_kmc::DEFAULT_PATH_TEMP
• command::featurise_kmc::DEFAULT_THREADS_READ
• command::featurise_kmc::DEFAULT_THREADS_WORK
• command::featurise_kmc::DEFAULT_THREADS_WRITE
• command::getraw::DEFAULT_CHEMISTRY
• command::getraw::DEFAULT_PATH_TEMP
• command::kraken::DEFAULT_PATH_TEMP
• command::mapcell::DEFAULT_PATH_TEMP
• command::minhash_hist::DEFAULT_PATH_TEMP
• command::query_fq::DEFAULT_PATH_TEMP
• command::query_kmc::DEFAULT_PATH_TEMP
• command::query_kmc::DEFAULT_THREADS_READ
• command::query_kmc::DEFAULT_THREADS_WORK
• command::query_kmc::DEFAULT_THREADS_WRITE
• command::shardify::DEFAULT_PATH_TEMP
• kmer::kmc_counter::HUGE_PAGE_SIZE
• kmer::kmc_counter::KMC_COUNTER_MAX_DIGITS