List of all items
Structs
- FlagFilter
- OutputWriter
- ReadsMapped
- bam_generator::BamFileNamedReader
- bam_generator::BamGeneratorSet
- bam_generator::FilteredBamReader
- bam_generator::NamedBamMaker
- bam_generator::NamedBamMakerGenerator
- bam_generator::StreamingFilteredNamedBamReader
- bam_generator::StreamingFilteredNamedBamReaderGenerator
- bam_generator::StreamingNamedBamReader
- bam_generator::StreamingNamedBamReaderGenerator
- cli::COVERM_CLUSTER_COMMAND_DEFINITION
- coverage_takers::CoverageEntry
- coverage_takers::CoverageTakerTypeIterator
- coverage_takers::EntryAndCoverages
- filter::ReferenceSortedBamFilter
- genome_exclusion::GenomesAndContigsExclusionFilter
- genome_exclusion::NoExclusionGenomeFilter
- genome_exclusion::SeparatorGenomeExclusionFilter
- genomes_and_contigs::GenomesAndContigs
- mapping_index_maintenance::PregeneratedStrobealignIndexStruct
- mapping_index_maintenance::TemporaryIndexStruct
- mapping_index_maintenance::VanillaIndexStruct
- mapping_parameters::MappingParameters
- mapping_parameters::OneSampleMappingParameters
- mapping_parameters::SingleReferenceMappingParameters
- shard_bam_reader::ReadSortedShardedBamReader
- shard_bam_reader::ShardedBamReader
- shard_bam_reader::ShardedBamReaderGenerator
Enums
- bam_generator::MappingProgram
- coverage_printer::CoveragePrinter
- coverage_takers::CoverageTakerType
- genome_exclusion::GenomeExcluders
- mapping_parameters::ReadFormat
- mosdepth_genome_coverage_estimators::CoverageEstimator
Traits
- bam_generator::NamedBamReader
- bam_generator::NamedBamReaderGenerator
- coverage_takers::CoverageTaker
- genome_exclusion::GenomeExclusion
- mapping_index_maintenance::MappingIndex
- mosdepth_genome_coverage_estimators::MosdepthGenomeCoverageEstimator
Functions
- bam_generator::build_mapping_command
- bam_generator::complete_processes
- bam_generator::generate_bam_maker_generator_from_reads
- bam_generator::generate_filtered_bam_readers_from_bam_files
- bam_generator::generate_filtered_named_bam_readers_from_reads
- bam_generator::generate_named_bam_readers_from_bam_files
- bam_generator::generate_named_bam_readers_from_reads
- cli::build_cli
- cli::contig_full_help
- cli::filter_full_help
- cli::genome_full_help
- cli::make_full_help
- contig::contig_coverage
- coverage_printer::print_dense_cached_coverage_taker
- coverage_printer::print_sparse_cached_coverage_taker
- external_command_checker::check_for_bwa
- external_command_checker::check_for_bwa_mem2
- external_command_checker::check_for_minimap2
- external_command_checker::check_for_samtools
- external_command_checker::check_for_strobealign
- genome::mosdepth_genome_coverage
- genome::mosdepth_genome_coverage_with_contig_names
- genome_parsing::read_genome_definition_file
- genome_parsing::read_genome_fasta_files
- genomes_and_contigs::find_first
- mapping_index_maintenance::check_reference_existence
- mapping_index_maintenance::generate_bwa_index
- mapping_index_maintenance::generate_concatenated_fasta_file
- mapping_index_maintenance::generate_minimap2_index
- shard_bam_reader::generate_named_sharded_bam_readers_from_reads
- shard_bam_reader::generate_sharded_bam_reader_from_bam_files