List of all items
Structs
- cleanup::AutoCleanFile
- collections_ext::counter::Counter
- ds::ReadInfo
- ds::region::Region
- ds::region::Regions
- fastx_reader::fasta_reader::FastaFileReader
- fastx_reader::fastq_reader::FastqReader
- file_reader::bed_reader::BedFileReaderIter
- file_reader::bed_reader::BedInfo
- file_reader::bed_reader::BedRowData
- file_reader::vcf_reader::VcfInfo
- file_reader::vcf_reader::VcfReaderIter
- file_reader::vcf_reader::VcfRowData
- gsbam::bam_header_ext::BamHeaderExt
- gsbam::bam_header_ext::HeaderSQ
- gsbam::bam_header_ext::PgHeader
- gsbam::bam_record_ext::BamRecordExt
- gsbam::cigar_ext::LongInsRegions
- gsbam::cigar_ext::RangeIdentityCalculator
- gsbam::plp_counts_from_records::PlpCnts
- gsbam::query_locus_blacklist_gen::LongInsBlacklist
- gsbam::query_locus_blacklist_gen::LowIdentityBlacklist
- poly_n::RefPolyLocusInfo
- sys_monitor::SysMon
- utils::Range
- utils::ScopedTimer
- utils::Timer
Enums
Traits
Functions
- dna::reverse_complement
- ds::idx2name_and_seq
- ds::name2idx
- ds::name2idx_and_seq
- ds::name2seq
- fastx_reader::fastx2bam::fasta2bam
- fastx_reader::fastx2bam::fastq2bam
- fastx_reader::fastx_header_line_to_header
- fastx_reader::read_fastx
- gsbam::bam_reader::read_records
- gsbam::bam_record_ext::draw_aligned_seq
- gsbam::bam_record_ext::record2str
- gsbam::build_pg_header
- gsbam::cigar_ext::compute_qstart_qend_with_cigar
- gsbam::cigar_ext::long_ins_regions_in_query
- gsbam::cigar_ext::parse_cigar_string
- gsbam::get_last_pg_from_bam_header
- gsbam::plp_counts_from_records::compute_max_ins_of_each_ref_position
- gsbam::plp_counts_from_records::get_base_idx
- gsbam::plp_counts_from_records::plp_with_records_region
- gsbam::plp_counts_from_records::plp_within_region
- gsbam::query_locus_blacklist_gen::get_query_locus_blacklist
- gsbam::read_bam
- gsbam::utils::seperate_dup_nondup_channels
- itertools::sliding_window
- matrix::transpose::transpose
- matrix::transpose::transpose_blocked
- pbar::get_bar_pb
- pbar::get_spin_pb
- phreq::phreq2err
- phreq::phreq2quality
- phreq::phreq_list_2_error_list
- phreq::phreq_list_2_quality
- phreq::phreq_list_2_quality_list
- phreq::quality_2_phreq
- phreq::quality_2_phreq_f32
- poly_n::extract_poly_locus_info_from_record
- poly_n::find_poly_n_regions
- poly_n::position_relation
- samtools::samtools_bai
- samtools::sort_by_coordinates
- samtools::sort_by_tag
- sys_monitor::get_thread_count
- utils::command_line_str
- utils::fastx_file_fmt
- utils::generate_tmp_filename
- utils::range_parser