List of all items
Structs
- annotation::Annotation
- annotation::GeneSpan
- circ_catalog::CircCatalogRecord
- ciri_as::AsConfig
- ciri_as::CohortAssembleConfig
- ciri_as::CohortAssembleSummary
- ciri_as::CohortSampleInput
- ciri_as::IsoformRunSummary
- ciri_as::SegmentRunSummary
- fasta::FastaReader
- index_compare::IndexCompare
- is_bsj_hg2::IsBSJHg2
- is_bsj_hg2::SmithWaterman
- scan1::Scan1
- scan2::CandidateBreakpoint
- scan2::Scan2
- scan2::Scan2SegmentArtifacts
- simulator::SimulateArgs
- simulator::SimulationSummary
- summary::Summary
- utils::AlignmentRecord
Enums
Functions
- circ_catalog::read_circ_bed6
- ciri_as::rebuild_major_isoforms_from_segments
- ciri_as::run_ciri_as
- ciri_as::run_ciri_assemble
- cli::assemble::main
- cli::ciri::main
- cli::merge::main
- cli::simulator::main
- is_bsj_hg2::java_substring
- is_bsj_hg2::report_scan1_hg_profile
- is_bsj_hg2::report_scan2_hg_profile
- misd::misd
- runtime::cli_trace_enabled
- runtime::emit_perf_line
- runtime::emit_trace_line
- runtime::init_runtime
- runtime::scan1_profile_enabled
- runtime::scan2_profile_enabled
- runtime::should_trace_read
- runtime::trace_hg2_enabled
- runtime::with_trace_hg2_scope
- sam_bam::check_bam_sorting
- sam_bam::detect_format
- simulator::run
- utils::alignment_short_cs
- utils::bam_shard_count
- utils::bsj1_path_for_output
- utils::bsj2_path_for_output
- utils::bsj_is_summary_priority
- utils::bsj_path_for_output
- utils::bsj_payload_start
- utils::clip_sequence_payload
- utils::fsj_path_for_output
- utils::is_bsj_mate_label
- utils::local_clip_evidence_lines
- utils::log_path_for_output
- utils::parse_cigar_ops_basic
- utils::parse_mem_str
- utils::part_path
- utils::perf_path_for_output
- utils::result_path_for_output
- utils::reverse_complement
- utils::segments1_path_for_output
- utils::segments2_path_for_output
- utils::segments_non_bsj_path_for_output
- utils::trace_path_for_output