Index

Symbols

2bit

_

__add__() (mavis.bam.stats.Histogram method) __and__() (mavis.interval.Interval method) __len__() (mavis.annotate.base.BioInterval method) (mavis.illustrate.util.LabelMapping method) (mavis.interval.Interval method)

__or__() (mavis.annotate.splicing.SpliceSite method) (mavis.interval.Interval method) __sub__() (mavis.interval.Interval method) __xor__() (mavis.interval.Interval method)

A

acceptor (mavis.annotate.genomic.Exon attribute) acceptor_splice_site (mavis.annotate.genomic.Exon attribute) add() (mavis.bam.stats.Histogram method) (mavis.constants.MavisNamespace method) (mavis.illustrate.util.LabelMapping method) (mavis.interval.IntervalMapping method) add_break1_split_read() (mavis.validate.call.EventCall method) add_break2_split_read() (mavis.validate.call.EventCall method) add_edge() (mavis.assemble.DeBruijnGraph method) add_flanking_support() (mavis.validate.call.EventCall method) add_gene() (mavis.annotate.variant.Annotation method) add_mapped_sequence() (mavis.assemble.Contig method) add_read() (mavis.bam.cache.BamCache method) add_semi_optional_argument() (in module mavis.config) add_spanning_read() (mavis.validate.call.EventCall method) add_stranded_information() (mavis.bam.stats.BamStats method) align_contigs() (in module mavis.align) align_seq() (mavis.annotate.protein.Domain method) aligner, [1] alignment_matches() (in module mavis.bam.cigar) all_pair_group_keys() (in module mavis.cluster.cluster) alphanumeric_choice() (in module mavis.summary.summary) annotate_dgv() (in module mavis.summary.summary)

annotate_events() (in module mavis.annotate.variant) Annotation (class in mavis.annotate.variant) annotation_figure annotation_figure_legend annotation_filters, [1] annotation_id annotation_memory, [1] assemble() (in module mavis.assemble) assemble_contig() (mavis.validate.base.Evidence method) assembly_include_flanking_pairs, [1] assembly_include_half_mapped_reads, [1] assembly_max_kmer_size, [1] assembly_max_kmer_strict, [1] assembly_max_paths, [1] assembly_min_edge_weight, [1] assembly_min_exact_match_to_remap, [1] assembly_min_nc_edge_weight, [1] assembly_min_remap_coverage, [1] assembly_min_remapped_seq, [1] assembly_min_tgt_to_exclude_half_map, [1] assembly_min_uniq, [1] assembly_strand_concordance, [1] augment_parser() (in module mavis.config)

B

bam BamCache (class in mavis.bam.cache) BamStats (class in mavis.bam.stats) bash_expands() (in module mavis.util) bed BioInterval (class in mavis.annotate.base) blat Blat (class in mavis.blat) blat_limit_top_aln, [1] blat_min_identity, [1] break1_chromosome break1_ewindow break1_ewindow_count break1_ewindow_practical_coverage break1_homologous_seq break1_orientation break1_position_end break1_position_start break1_seq break1_split_reads break1_split_reads_forced break1_strand break1_tgt_align_split_read_names() (mavis.validate.call.EventCall method) break2_chromosome break2_ewindow break2_ewindow_count

break2_ewindow_practical_coverage break2_homologous_seq break2_orientation break2_position_end break2_position_start break2_seq break2_split_reads break2_split_reads_forced break2_strand break2_tgt_align_split_read_names() (mavis.validate.call.EventCall method) breakpoint Breakpoint (class in mavis.breakpoint) breakpoint pair breakpoint_color, [1] breakpoint_contig_remapped_depth() (mavis.align.SplitAlignment static method) breakpoint_pos() (in module mavis.bam.read) breakpoint_sequence_homology() (mavis.breakpoint.BreakpointPair method) BreakpointPair (class in mavis.breakpoint) BreakpointPairGroupKey (class in mavis.cluster.cluster) build() (mavis.annotate.variant.FusionTranscript class method) (mavis.config.LibraryConfig static method) build_annotate_command() (in module mavis.main) build_dependency_string() (in module mavis.submit) build_header() (mavis.submit.SubmissionScript method) build_validate_command() (in module mavis.main) BWA

C

calculate_alignment_score() (in module mavis.bam.read) calculate_orf() (in module mavis.annotate.protein) call_breakpoint_pair() (mavis.breakpoint.BreakpointPair class method) call_error, [1] call_events() (in module mavis.validate.call) call_method CALL_METHOD (in module mavis.constants) cast() (in module mavis.util) cast_if_not_none() (in module mavis.config) cdna_synon center (mavis.interval.Interval attribute) check_completion() (in module mavis.checker) choose_more_annotated() (in module mavis.annotate.variant) choose_transcripts_by_priority() (in module mavis.annotate.variant) chr (mavis.annotate.genomic.Gene attribute) (mavis.annotate.genomic.IntergenicRegion attribute) ChrListString (class in mavis.util) CIGAR (in module mavis.constants) classify() (mavis.annotate.splicing.SplicingPattern static method) (mavis.breakpoint.BreakpointPair class method) close() (mavis.bam.cache.BamCache method) cluster_id cluster_initial_size_limit, [1] cluster_radius, [1] cluster_size CODON_SIZE (in module mavis.constants) collect_compatible_flanking_pair() (mavis.validate.base.Evidence method) collect_flanking_pair() (mavis.validate.base.Evidence method) collect_from_outer_window() (mavis.validate.base.Evidence method) collect_half_mapped() (mavis.validate.base.Evidence method) collect_log() (mavis.checker.PipelineStageRun method) collect_spanning_read() (mavis.validate.base.Evidence method) collect_split_read() (mavis.validate.base.Evidence method) collect_stamp() (mavis.checker.PipelineStageRun method) COLUMNS (in module mavis.constants) comparison_distance() (in module mavis.pairing.pairing) compatible_window1 (mavis.validate.base.Evidence attribute) compatible_window2 (mavis.validate.base.Evidence attribute) compute() (in module mavis.bam.cigar) compute_exonic_distance() (mavis.validate.evidence.TranscriptomeEvidence static method) compute_fragment_size() (mavis.validate.base.Evidence method) (mavis.validate.evidence.GenomeEvidence method) (mavis.validate.evidence.TranscriptomeEvidence method) compute_genome_bam_stats() (in module mavis.bam.stats) compute_transcriptome_bam_stats() (in module mavis.bam.stats)

Contig (class in mavis.assemble) contig_alignment_cigar contig_alignment_query_name contig_alignment_reference_start contig_alignment_score contig_aln_max_event_size, [1] contig_aln_merge_inner_anchor, [1] contig_aln_merge_outer_anchor, [1] contig_aln_min_anchor_size, [1] contig_aln_min_query_consumption, [1] contig_build_score contig_call_distance, [1] contig_remap_coverage contig_remap_score contig_remapped_read_names contig_remapped_reads contig_seq contig_strand_specific contigs_aligned contigs_assembled convert_aa_to_cdna() (mavis.annotate.protein.Translation method) convert_cdna_to_aa() (mavis.annotate.protein.Translation method) convert_cdna_to_genomic() (mavis.annotate.genomic.Transcript method) (mavis.annotate.genomic.UsTranscript method) convert_events_to_softclipping() (in module mavis.bam.read) convert_for_igv() (in module mavis.bam.cigar) convert_genomic_to_cdna() (mavis.annotate.genomic.Transcript method) (mavis.annotate.genomic.UsTranscript method) convert_genomic_to_cds() (mavis.annotate.protein.Translation method) convert_genomic_to_cds_notation() (mavis.annotate.protein.Translation method) convert_genomic_to_nearest_cdna() (mavis.annotate.genomic.Transcript method) (mavis.annotate.genomic.UsTranscript method) convert_genomic_to_nearest_cds() (mavis.annotate.protein.Translation method) convert_main() (in module mavis.main) convert_pos() (mavis.interval.Interval class method) (mavis.interval.IntervalMapping method) convert_ratioed_pos() (mavis.interval.Interval class method) convert_set_to_ranges() (in module mavis.checker) convert_string_to_cigar() (in module mavis.bam.cigar) convert_tab_to_json() (in module mavis.annotate.file_io) convert_tool_output() (in module mavis.tools) copy() (mavis.bam.read.SamRead class method) (mavis.breakpoint.BreakpointPair method) (mavis.validate.base.Evidence method) copy_onto() (mavis.bam.read.SamRead class method) CustomHelpFormatter (class in mavis.config)

D

DeBruijnGraph (class in mavis.assemble) decide_sequenced_strand() (mavis.validate.base.Evidence method) DEFAULTS (in module mavis.annotate.constants) (in module mavis.cluster.constants) (in module mavis.illustrate.constants) (in module mavis.pairing.constants) (in module mavis.summary.constants) (in module mavis.validate.constants) define() (mavis.constants.MavisNamespace method) determine_prime() (in module mavis.annotate.variant) devnull() (in module mavis.util) DiagramSettings (class in mavis.illustrate.constants) digraph_connected_components() (in module mavis.assemble) DISEASE_STATUS (in module mavis.constants) dist() (mavis.interval.Interval class method) distribution_stderr() (mavis.bam.stats.Histogram method) Domain (class in mavis.annotate.protein) domain_color, [1] domain_mismatch_color, [1] domain_name_regex_filter, [1] domain_scaffold_color, [1]

DomainRegion (class in mavis.annotate.protein) donor (mavis.annotate.genomic.Exon attribute) donor_splice_site (mavis.annotate.genomic.Exon attribute) draw() (in module mavis.annotate.main) draw_breakpoint() (in module mavis.illustrate.elements) draw_exon() (in module mavis.illustrate.elements) draw_exon_track() (in module mavis.illustrate.elements) draw_fusions_only, [1] draw_gene() (in module mavis.illustrate.elements) draw_genes() (in module mavis.illustrate.elements) draw_legend() (in module mavis.illustrate.elements) draw_multi_transcript_overlay() (in module mavis.illustrate.diagram) draw_scatter() (in module mavis.illustrate.scatter) draw_sv_summary_diagram() (in module mavis.illustrate.diagram) draw_template() (in module mavis.illustrate.elements) draw_transcript_with_translation() (in module mavis.illustrate.elements) draw_ustranscript() (in module mavis.illustrate.elements) draw_vmarker() (in module mavis.illustrate.elements) drawing_width_iter_increase, [1] DrawingFitError dynamic_label_color() (in module mavis.illustrate.util)

E

end (mavis.annotate.base.BioInterval attribute) enforce() (mavis.constants.MavisNamespace method) equivalent() (in module mavis.pairing.pairing) estimate_run_time() (mavis.checker.PipelineStageRun method) event event type

event_type EventCall (class in mavis.validate.call) Evidence (class in mavis.validate.base) Exon (class in mavis.annotate.genomic) exon_number() (mavis.annotate.genomic.UsTranscript method) (mavis.annotate.variant.FusionTranscript method) extend_softclipping() (in module mavis.bam.cigar)

F

fasta fetch() (mavis.bam.cache.BamCache method) fetch_from_bins() (mavis.bam.cache.BamCache method) fetch_method_individual, [1] fetch_min_bin_size, [1] fetch_reads_bins, [1] fetch_reads_limit, [1] filter_by_annotations() (in module mavis.summary.summary) filter_by_call_method() (in module mavis.summary.summary) filter_by_evidence() (in module mavis.summary.summary) filter_cdna_synon, [1] filter_consumed_pairs() (in module mavis.validate.call) filter_contigs() (in module mavis.assemble) filter_min_flanking_reads, [1] filter_min_linking_split_reads, [1] filter_min_remapped_reads, [1] filter_min_spanning_reads, [1] filter_min_split_reads, [1] filter_on_overlap() (in module mavis.util) filter_protein_synon, [1] filter_secondary_alignments, [1] filter_uninformative() (in module mavis.util) flanking read pair

flanking_call_distance, [1] flanking_median_fragment_size flanking_metrics() (mavis.validate.call.EventCall method) flanking_pairs flanking_pairs_compatible flanking_stdev_fragment_size flatten() (mavis.annotate.variant.Annotation method) (mavis.breakpoint.BreakpointPair method) (mavis.config.LibraryConfig method) (mavis.constants.MavisNamespace method) (mavis.validate.base.Evidence method) (mavis.validate.call.EventCall method) flatten_fusion_transcript() (in module mavis.annotate.variant) flatten_fusion_translation() (in module mavis.annotate.variant) float_fraction() (in module mavis.constants) full_pog (module) fusion_cdna_coding_end, [1] fusion_cdna_coding_start fusion_mapped_domains fusion_sequence_fasta_file fusion_sequence_fasta_id fusion_splicing_pattern FusionTranscript (class in mavis.annotate.variant) fuzzy_mismatch_number, [1]

G

Gene (class in mavis.annotate.genomic) gene (mavis.annotate.genomic.UsTranscript attribute) gene1 gene1_aliases gene1_color, [1] gene1_color_selected, [1] gene1_direction gene2 gene2_aliases gene2_color, [1] gene2_color_selected, [1] gene2_direction gene_product_type GENE_PRODUCT_TYPE (in module mavis.constants) generate_complete_stamp() (in module mavis.util) generate_config() (in module mavis.config) generate_interval_mapping() (in module mavis.illustrate.util) generate_splicing_patterns() (mavis.annotate.genomic.UsTranscript method) genes_encompassed genes_overlapping_break1 genes_overlapping_break2 genes_proximal_to_break1 genes_proximal_to_break2 GenomeEvidence (class in mavis.validate.evidence) get() (mavis.constants.MavisNamespace method) get_aa_seq() (mavis.annotate.protein.Translation method) get_bam_file() (in module full_pog) get_bed_repesentation() (mavis.breakpoint.BreakpointPair method) (mavis.validate.base.Evidence method) (mavis.validate.call.EventCall method)

get_blat_version() (in module mavis.blat) get_cdna_seq() (mavis.annotate.genomic.UsTranscript method) (mavis.annotate.variant.FusionTranscript method) get_cds_seq() (mavis.annotate.protein.Translation method) get_chr() (mavis.annotate.base.BioInterval method) get_edge_freq() (mavis.assemble.DeBruijnGraph method) get_env_variable() (in module mavis.util) get_key() (mavis.illustrate.util.LabelMapping method) get_libraries() (in module full_pog) get_mate() (mavis.bam.cache.BamCache method) get_metavar() (in module mavis.config) get_pairing_state() (in module mavis.summary.summary) get_read_reference_name() (mavis.bam.cache.BamCache method) get_samtools_version() (in module mavis.bam.read) get_seq() (mavis.annotate.base.BioInterval method) (mavis.annotate.genomic.Gene method) (mavis.annotate.genomic.Transcript method) (mavis.annotate.genomic.UsTranscript method) (mavis.annotate.protein.Translation method) (mavis.annotate.variant.FusionTranscript method) get_seqs() (mavis.annotate.protein.Domain method) get_sinks() (mavis.assemble.DeBruijnGraph method) get_sources() (mavis.assemble.DeBruijnGraph method) get_strand() (mavis.annotate.base.BioInterval method) get_xml() (mavis.illustrate.util.Tag method) GIEMSA_STAIN (in module mavis.constants) group_events() (in module mavis.summary.summary)

H

half-mapped read has_compatible (mavis.validate.call.EventCall attribute) has_read() (mavis.bam.cache.BamCache method)

has_transcriptome() (mavis.config.MavisConfig method) HGVS hgvs_standardize_cigar() (in module mavis.bam.cigar) Histogram (class in mavis.bam.stats)

I

IGV IGV batch file import_env, [1] inferred_equivalent() (in module mavis.pairing.pairing) inferred_pairing inner_window1 (mavis.validate.base.Evidence attribute) inner_window2 (mavis.validate.base.Evidence attribute) input_call_distance, [1] interchromosomal (mavis.breakpoint.BreakpointPair attribute)

IntergenicRegion (class in mavis.annotate.genomic) intersection() (mavis.interval.Interval class method) Interval (class in mavis.interval) IntervalMapping (class in mavis.interval) InvalidRearrangement is_reverse (mavis.annotate.base.BioInterval attribute) is_trans() (mavis.config.LibraryConfig method) items() (mavis.constants.MavisNamespace method) (mavis.illustrate.util.LabelMapping method)

J

join() (in module mavis.bam.cigar)

JSON

K

key (mavis.breakpoint.Breakpoint attribute) key() (mavis.annotate.base.BioInterval method) (mavis.annotate.genomic.Gene method) (mavis.annotate.genomic.IntergenicRegion method) (mavis.annotate.protein.Domain method) (mavis.annotate.protein.Translation method)

keys() (mavis.constants.MavisNamespace method) kmers() (in module mavis.assemble)

L

label_color, [1] LabelMapping (class in mavis.illustrate.util) length() (mavis.interval.Interval method) library LibraryConfig (class in mavis.config) LibraryRun (class in mavis.checker) limit_to_chr, [1] linking_split_read_names() (mavis.validate.call.EventCall method) linking_split_reads load_annotations() (in module mavis.annotate.file_io)

load_evidence() (mavis.validate.base.Evidence method) load_masking_regions() (in module mavis.annotate.file_io) load_multiple() (mavis.validate.base.Evidence class method) load_reference_genes() (in module mavis.annotate.file_io) load_reference_genome() (in module mavis.annotate.file_io) load_templates() (in module mavis.annotate.file_io) log() (in module mavis.util) log_arguments() (in module mavis.util) LogDetails (class in mavis.checker) longest_exact_match() (in module mavis.bam.cigar) longest_fuzzy_match() (in module mavis.bam.cigar)

M

main() (in module full_pog) (in module mavis.annotate.main) (in module mavis.cluster.main) (in module mavis.main) (in module mavis.pairing.main) (in module mavis.summary.main) (in module mavis.validate.main) main_pipeline() (in module mavis.main) map_ref_range_to_query_range() (in module mavis.bam.read) map_region_to_genome() (mavis.annotate.variant.FusionTranscript method) mask_fill, [1] mask_opacity, [1] match_percent() (in module mavis.bam.cigar) mavis (module), [1] mavis.align (module) mavis.annotate (module), [1] mavis.annotate.base (module) mavis.annotate.constants (module) mavis.annotate.file_io (module) mavis.annotate.genomic (module) mavis.annotate.main (module) mavis.annotate.protein (module) mavis.annotate.splicing (module) mavis.annotate.variant (module) mavis.assemble (module) mavis.bam (module), [1] mavis.bam.cache (module) mavis.bam.cigar (module) mavis.bam.read (module) mavis.bam.stats (module) mavis.blat (module) mavis.breakpoint (module) mavis.checker (module) mavis.cluster (module), [1] mavis.cluster.cluster (module) mavis.cluster.constants (module) mavis.cluster.main (module) mavis.config (module) mavis.constants (module) mavis.error (module) mavis.illustrate (module), [1] mavis.illustrate.constants (module) mavis.illustrate.diagram (module) mavis.illustrate.elements (module) mavis.illustrate.scatter (module) mavis.illustrate.util (module) mavis.interval (module) mavis.main (module) mavis.pairing (module), [1]

mavis.pairing.constants (module) mavis.pairing.main (module) mavis.pairing.pairing (module) mavis.submit (module) mavis.summary (module), [1] mavis.summary.constants (module) mavis.summary.main (module) mavis.summary.summary (module) mavis.tools (module) mavis.util (module) mavis.validate (module), [1] mavis.validate.base (module) mavis.validate.call (module) mavis.validate.constants (module) mavis.validate.evidence (module) mavis.validate.main (module) MavisConfig (class in mavis.config) MavisNamespace (class in mavis.constants) max_drawing_retries, [1] max_expected_fragment_size (mavis.validate.base.Evidence attribute) max_files, [1] max_orf_cap, [1] max_proximity, [1] max_sc_preceeding_anchor, [1] median() (mavis.bam.stats.Histogram method) memory_limit, [1] merge_breakpoint_pairs() (in module mavis.cluster.cluster) merge_by_union() (in module mavis.cluster.cluster) merge_indels() (in module mavis.bam.cigar) merge_integer_intervals() (in module mavis.cluster.cluster) merge_internal_events() (in module mavis.bam.cigar) millibad() (mavis.blat.Blat static method) min_anchor_exact, [1] min_anchor_fuzzy, [1] min_anchor_match, [1] min_clusters_per_file, [1] min_domain_mapping_match, [1] min_double_aligned_to_estimate_insertion_size, [1] min_expected_fragment_size (mavis.validate.base.Evidence attribute) min_flanking_pairs_resolution, [1] min_linking_split_reads, [1] min_mapping_quality, [1] min_non_target_aligned_split_reads, [1] min_nonoverlapping() (mavis.interval.Interval class method) min_orf_size, [1] min_sample_size_to_apply_percentage, [1] min_softclipping, [1] min_spanning_reads_resolution, [1] min_splits_reads_resolution, [1] mkdirp() (in module mavis.util)

N

NA_MAPPING_QUALITY (in module mavis.constants) next_reference_name (mavis.bam.read.SamRead attribute)

NotSpecifiedError novel_exon_color, [1] nsb_align() (in module mavis.bam.read)

O

opposing_strands (mavis.align.SplitAlignment attribute) OPTIONS (in module mavis.submit) ORIENT (in module mavis.constants) orientation_supports_type() (in module mavis.bam.read) outer_window1 (mavis.validate.base.Evidence attribute)

outer_window2 (mavis.validate.base.Evidence attribute) outer_window_min_event_size, [1] output_tabbed_file() (in module mavis.util) overlapping_transcripts() (in module mavis.annotate.variant) overlaps() (mavis.interval.Interval class method) overlay_main() (in module mavis.main)

P

pair_key() (in module mavis.cluster.cluster) pairing parse_annotations_json() (in module mavis.annotate.file_io) parse_args() (mavis.config.LibraryConfig class method) parse_overlay_args() (in module mavis.main) parse_run_time() (in module mavis.checker) percent_identity() (mavis.blat.Blat static method) PipelineStageRun (class in mavis.checker) position_in_range() (mavis.interval.Interval class method) predict_splice_sites() (in module mavis.annotate.splicing) predict_transcriptome_breakpoint() (in module mavis.pairing.pairing)

PRIME (in module mavis.constants) process_blat_output() (in module mavis.blat) product_id protein_synon protocol PROTOCOL (in module mavis.constants) psl pslx pslx_row_to_pysam() (mavis.blat.Blat static method) pull_contigs_from_component() (in module mavis.assemble) putative_event_types() (mavis.validate.base.Evidence method) PYSAM_READ_FLAGS (in module mavis.constants)

Q

query_consumption() (mavis.align.SplitAlignment method) query_coverage() (mavis.align.SplitAlignment method) query_coverage_interval() (in module mavis.align)

query_coverage_read1() (mavis.align.SplitAlignment method) query_coverage_read2() (mavis.align.SplitAlignment method) query_overlap_extension() (mavis.align.SplitAlignment method) queue, [1]

R

RangeAppendAction (class in mavis.config) raw_break1_split_reads raw_break2_split_reads raw_flanking_pairs raw_spanning_reads read() (mavis.config.MavisConfig static method) read_bpp_from_input_file() (in module mavis.util) read_inputs() (in module mavis.util) read_pair_type() (in module mavis.bam.read) read_pslx() (mavis.blat.Blat static method) recompute_cigar_mismatch() (in module mavis.bam.cigar)

reference_id() (mavis.bam.cache.BamCache method) reference_name (mavis.bam.read.SamRead attribute) ReferenceName (class in mavis.annotate.base) remap_coverage() (mavis.assemble.Contig method) remap_depth() (mavis.assemble.Contig method) remap_score() (mavis.assemble.Contig method) report() (mavis.checker.LibraryRun method) (mavis.checker.PipelineStageRun method) reserved_attr (mavis.constants.MavisNamespace attribute) reverse() (mavis.constants.MavisNamespace method) reverse_complement() (in module mavis.constants) run_conversion() (in module mavis.main)

S

SamRead (class in mavis.bam.read) samtools_v0_sort() (in module mavis.bam.read) samtools_v1_sort() (in module mavis.bam.read) sc_extension_stop, [1] scaffold_color, [1] ScatterPlot (class in mavis.illustrate.scatter) scheduler, [1] SCHEDULER (in module mavis.submit) score() (in module mavis.bam.cigar) (mavis.align.SplitAlignment method) (mavis.blat.Blat static method) score_region_mapping() (mavis.annotate.protein.Domain method) select_supporting_alignments() (mavis.align.SplitAlignment static method) sequenced_strand() (in module mavis.bam.read) set_key() (mavis.illustrate.util.LabelMapping method) SGE SLURM smallest_nonoverlapping_repeat() (in module mavis.bam.cigar) soft_cast() (in module mavis.util) soft_cast_null() (in module mavis.summary.main) sort_columns() (in module mavis.constants) spanning read spanning_call_distance, [1] spanning_read_names spanning_reads splice_color, [1] SPLICE_SITE_RADIUS (in module mavis.annotate.constants)

SPLICE_TYPE (in module mavis.annotate.constants) spliced_transcripts (mavis.annotate.genomic.Gene attribute) SpliceSite (class in mavis.annotate.splicing) SplicingPattern (class in mavis.annotate.splicing) split read split_call_distance, [1] split_clusters() (in module mavis.cluster.main) split_intervals_into_tracks() (in module mavis.illustrate.util) split_overlap() (mavis.interval.Interval class method) SplitAlignment (class in mavis.align) standardize_read() (mavis.validate.base.Evidence method) start (mavis.annotate.base.BioInterval attribute) START_AA (in module mavis.constants) stdev_count_abnormal, [1] STOP_AA (in module mavis.constants) STRAND (in module mavis.constants) strand_determining_read, [1] stranded structural variant SUBCOMMAND (in module mavis.constants) SubmissionScript (class in mavis.submit) support() (mavis.validate.call.EventCall method) SUPPORTED_ALIGNER (in module mavis.align) SUPPORTED_TOOL (in module mavis.tools) supporting_reads() (mavis.validate.base.Evidence method) SVG SVTYPE (in module mavis.constants)

T

Tag (class in mavis.illustrate.util) Template (class in mavis.annotate.genomic) time_limit, [1] to_dict() (mavis.annotate.base.BioInterval method) (mavis.annotate.genomic.Gene method) (mavis.annotate.genomic.IntergenicRegion method) (mavis.breakpoint.Breakpoint method) tools tracking_id trans_validation_memory, [1] Transcript (class in mavis.annotate.genomic) transcript (mavis.annotate.genomic.Exon attribute) (mavis.annotate.protein.Translation attribute) transcript1

transcript2 transcript_priority() (mavis.annotate.genomic.Gene method) TranscriptomeEvidence (class in mavis.validate.evidence) transcripts (mavis.annotate.genomic.Gene attribute) (mavis.annotate.genomic.UsTranscript attribute) translate() (in module mavis.constants) Translation (class in mavis.annotate.protein) translation (mavis.annotate.protein.Domain attribute) translations (mavis.annotate.genomic.Gene attribute) (mavis.annotate.genomic.UsTranscript attribute) traverse_exonic_distance() (mavis.validate.evidence.TranscriptomeEvidence static method) trim_forks_by_freq() (mavis.assemble.DeBruijnGraph method) trim_noncutting_paths_by_freq() (mavis.assemble.DeBruijnGraph method) trim_tails_by_freq() (mavis.assemble.DeBruijnGraph method) type() (mavis.constants.MavisNamespace method)

U

uninformative_filter, [1] union() (mavis.interval.Interval class method) unique_exists() (in module mavis.util)

unspliced_transcript (mavis.annotate.genomic.Transcript attribute) untemplated_seq UsTranscript (class in mavis.annotate.genomic)

V

valid_chr() (mavis.bam.cache.BamCache method) validate_section() (in module mavis.config)

validation_id validation_memory, [1] values() (mavis.constants.MavisNamespace method)

W

WeakMavisNamespace (class in mavis.util) weighted_mean() (in module mavis.cluster.cluster) width, [1]

write() (mavis.submit.SubmissionScript method) write_bed_file() (in module mavis.util) write_config() (in module mavis.config)