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_seq() (mavis.annotate.protein.Domain method) align_sequences() (in module mavis.align) aligner, [1] alignment_id (mavis.bam.read.SamRead attribute) 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] assert_equal_attributes() (in module mavis.util) 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.fusion.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_error, [1] call_events() (in module mavis.validate.call) call_method CALL_METHOD (in module mavis.constants) call_paired_read_event() (in module mavis.align) call_protein_indel() (in module mavis.annotate.variant) call_read_events() (in module mavis.align) 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 class 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) compute() (in module mavis.bam.cigar) 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_extend_overlap, [1] contig_aln_min_query_consumption, [1] contig_aln_min_score, [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.PreTranscript method) (mavis.annotate.genomic.Transcript method) convert_cigar_to_string() (in module mavis.bam.cigar) convert_events_to_softclipping() (in module mavis.bam.read) convert_for_igv() (in module mavis.bam.cigar) convert_genomic_to_cdna() (mavis.annotate.genomic.PreTranscript method) (mavis.annotate.genomic.Transcript 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.PreTranscript method) (mavis.annotate.genomic.Transcript 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_to_duplication() (in module mavis.align) 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) deletion_sequences() (mavis.bam.read.SamRead method) determine_prime() (in module mavis.annotate.fusion) 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) distance() (mavis.validate.base.Evidence static method) (mavis.validate.evidence.TranscriptomeEvidence 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_non_synonymous_cdna_only, [1] 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_boundary_shift_cigar() (mavis.validate.evidence.TranscriptomeEvidence method) exon_number() (mavis.annotate.fusion.FusionTranscript method) (mavis.annotate.genomic.PreTranscript 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_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) from_iterable() (mavis.interval.Interval class method) fusion_cdna_coding_end, [1] fusion_cdna_coding_start fusion_mapped_domains fusion_protein_hgvs fusion_sequence_fasta_file fusion_sequence_fasta_id fusion_splicing_pattern FusionTranscript (class in mavis.annotate.fusion) fuzzy_mismatch_number, [1]

G

Gene (class in mavis.annotate.genomic) gene (mavis.annotate.genomic.PreTranscript 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_patterns() (mavis.annotate.splicing.SplicingPattern class method) generate_splicing_patterns() (mavis.annotate.genomic.PreTranscript method) generate_window() (mavis.validate.evidence.GenomeEvidence method) (mavis.validate.evidence.TranscriptomeEvidence 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_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.fusion.FusionTranscript method) (mavis.annotate.genomic.PreTranscript 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_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.fusion.FusionTranscript method) (mavis.annotate.genomic.Gene method) (mavis.annotate.genomic.PreTranscript method) (mavis.annotate.genomic.Transcript method) (mavis.annotate.protein.Translation 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_protein_notation() (mavis.annotate.variant.IndelCall method) hgvs_standardize_cigar() (in module mavis.bam.cigar) Histogram (class in mavis.bam.stats)

I

IGV IGV batch file import_env, [1] IndelCall (class in mavis.annotate.variant) inferred_equivalent() (in module mavis.pairing.pairing) inferred_pairing input_call_distance, [1] insertion_sequences() (mavis.bam.read.SamRead method) 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_putative_indel (mavis.breakpoint.BreakpointPair attribute) 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_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 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.fusion.FusionTranscript method) mapping_quality() (mavis.align.SplitAlignment 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.fusion (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_cds_shift() (mavis.validate.evidence.TranscriptomeEvidence method) 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) net_size net_size() (mavis.breakpoint.BreakpointPair method)

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

O

opposing_strands OPTIONS (in module mavis.submit) ORIENT (in module mavis.constants) orientation_supports_type() (in module mavis.bam.read)

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) PreTranscript (class in mavis.annotate.genomic)

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_length (mavis.bam.read.SamRead attribute) 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_breakpoint() (in module mavis.align) 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) 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_contig_alignments() (in module mavis.align) sequenced_strand() (in module mavis.bam.read) set_key() (mavis.illustrate.util.LabelMapping method) SGE single_transcript() (mavis.annotate.variant.Annotation method) SLURM 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) (mavis.validate.evidence.TranscriptomeEvidence 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.PreTranscript 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.PreTranscript attribute) traverse() (mavis.validate.base.Evidence static method) (mavis.validate.evidence.TranscriptomeEvidence 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

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)