Index

Symbols

2bit

_

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

__or__() (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.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 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_id assemble() (in module mavis.assemble) assemble_contig() (mavis.validate.base.Evidence method) assembly_include_flanking_pairs assembly_max_kmer_size assembly_max_kmer_strict assembly_max_paths assembly_min_edge_weight assembly_min_nc_edge_weight assembly_min_remap_coverage assembly_min_remapped_seq assembly_strand_concordance 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_min_identity blat_min_percent_of_max_score break1_call_method 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_call_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_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 class method)

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 call_events() (in module mavis.validate.call) CALL_METHOD (in module mavis.constants) cast() (in module mavis.config) cdna_synon center (mavis.interval.Interval attribute) check_completion() (in module mavis.main) check_library_dir() (in module mavis.main) check_single_job() (in module mavis.main) 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.breakpoint.BreakpointPair class method) close() (mavis.bam.cache.BamCache method) cluster_id 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_spanning_read() (mavis.validate.base.Evidence method) collect_split_read() (mavis.validate.base.Evidence method) COLUMNS (in module mavis.constants) 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 contig_aln_merge_inner_anchor contig_aln_min_anchor_size contig_aln_min_exact_block_event_merge contig_aln_min_query_consumption contig_build_score contig_call_distance: 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_pos() (mavis.interval.Interval class method) (mavis.interval.IntervalMapping method) convert_ratioed_pos() (mavis.interval.Interval class method) 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) copyOnto() (mavis.bam.read.SamRead class method)

D

DeBruijnGraph (class in mavis.assemble) decide_sequenced_strand() (mavis.validate.base.Evidence method) DEFAULTS (in module mavis.pairing.constants) (in module mavis.validate.constants) 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) distance() (in module mavis.validate.call) distribution_stderr() (mavis.bam.stats.Histogram method) Domain (class in mavis.annotate.protein) DomainRegion (class in mavis.annotate.protein) donor (mavis.annotate.genomic.Exon attribute)

donor_splice_site (mavis.annotate.genomic.Exon attribute) draw_breakpoint() (in module mavis.illustrate.elements) draw_exon() (in module mavis.illustrate.elements) draw_exon_track() (in module mavis.illustrate.elements) 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) DrawingFitError dynamic_label_color() (in module mavis.illustrate.util)

E

end (mavis.annotate.base.BioInterval attribute) end_splice_site (mavis.annotate.genomic.Exon attribute) equivalent_events() (in module mavis.pairing.pairing) 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_min_bin_size fetch_reads_bins fetch_reads_limit 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_consumed_pairs() (in module mavis.validate.call) filter_on_overlap() (in module mavis.util) filter_secondary_alignments filter_uninformative() (in module mavis.util) flanking read pair flanking_call_distance: 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.JobSchedulingConfig method) (mavis.config.LibraryConfig method) (mavis.config.PairingConfig method) (mavis.config.ReferenceFilesConfig method) (mavis.config.SummaryConfig 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) fusion_cdna_coding_end fusion_cdna_coding_start fusion_mapped_domains fusion_sequence_fasta_file fusion_sequence_fasta_id fusion_splicing_pattern FusionTranscript (class in mavis.annotate.variant)

G

Gene (class in mavis.annotate.genomic) gene (mavis.annotate.genomic.usTranscript attribute) gene1 gene1_aliases gene1_direction gene2 gene2_aliases gene2_direction gene_product_type GENE_PRODUCT_TYPE (in module mavis.constants) generate_complete_stamp() (in module mavis.util) generate_config() (in module mavis.main) 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_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.genomic.usTranscript 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.config) get_key() (mavis.illustrate.util.LabelMapping method) get_mate() (mavis.bam.cache.BamCache method) 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_spliced_cdna_seq() (mavis.annotate.variant.FusionTranscript method) get_strand() (mavis.annotate.base.BioInterval method) get_xml() (mavis.illustrate.util.Tag method) GIESMA_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) hgvs_standardize_cigar() (in module mavis.bam.cigar) Histogram (class in mavis.bam.stats)

I

IGV IGV batch file inner_window1 (mavis.validate.base.Evidence attribute) inner_window2 (mavis.validate.base.Evidence attribute) 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 items() (mavis.illustrate.util.LabelMapping method) (mavis.util.MavisNamespace method)

J

JobSchedulingConfig (class in mavis.config)

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)

kmers() (in module mavis.assemble)

L

LabelMapping (class in mavis.illustrate.util) length() (mavis.interval.Interval method) library LibraryConfig (class in mavis.config) 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) 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_region_to_genome() (mavis.annotate.variant.FusionTranscript method) 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.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.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.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) mavis.version (module) MavisNamespace (class in mavis.util) max_expected_fragment_size (mavis.validate.base.Evidence attribute) max_sc_preceeding_anchor median() (mavis.bam.stats.Histogram method) median_fragment_size 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_double_aligned_to_estimate_insertion_size min_expected_fragment_size (mavis.validate.base.Evidence attribute) min_flanking_pairs_resolution min_linking_split_reads min_mapping_quality min_non_target_aligned_split_reads min_nonoverlapping() (mavis.interval.Interval class method) min_softclipping min_splits_reads_resolution mkdirp() (in module mavis.util)

N

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

NotSpecifiedError nsb_align() (in module mavis.bam.read)

O

opposing_strands 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 output_tabbed_file() (in module mavis.util) overlapping_transcripts() (in module mavis.annotate.variant) overlaps() (mavis.interval.Interval class method)

P

pair_key() (in module mavis.cluster.cluster) paired_alignment_score() (in module mavis.align) pairing PairingConfig (class in mavis.config) parse_annotations_json() (in module mavis.annotate.file_io) parse_runtime_from_log() (in module mavis.main) percent_identity() (mavis.blat.Blat static method) position_in_range() (mavis.interval.Interval class method) predict_transcriptome_breakpoint() (in module mavis.pairing.pairing) PRIME (in module mavis.constants)

print_incomplete_log_details() (in module mavis.main) 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_coverage_interval() (in module mavis.align)

R

raw_break1_split_reads raw_break2_split_reads raw_flanking_pairs raw_spanning_reads read_bpp_from_input_file() (in module mavis.breakpoint) read_config() (in module mavis.config) read_inputs() (in module mavis.util) read_length

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) ReferenceFilesConfig (class in mavis.config) ReferenceName (class in mavis.annotate.base) remap_score() (mavis.assemble.Contig method) reverse_complement() (in module mavis.constants)

S

SamRead (class in mavis.bam.read) samtools_v0_sort() (in module mavis.bam.read) samtools_v1_sort() (in module mavis.bam.read) ScatterPlot (class in mavis.illustrate.scatter) score() (in module mavis.bam.cigar) (mavis.blat.Blat static method) score_region_mapping() (mavis.annotate.protein.Domain method) select_paired_alignments() (in module mavis.align) sequenced_strand() (in module mavis.bam.read) set_key() (mavis.illustrate.util.LabelMapping method) smallest_nonoverlapping_repeat() (in module mavis.bam.cigar) sort_columns() (in module mavis.constants) spanning read spanning_call_distance: spanning_read_names spanning_reads SPLICE_SITE_RADIUS (in module mavis.constants) SPLICE_TYPE (in module mavis.constants) spliced_transcripts (mavis.annotate.genomic.Gene attribute) SplicingPattern (class in mavis.annotate.genomic)

split read split_call_distance: split_intervals_into_tracks() (in module mavis.illustrate.util) split_overlap() (mavis.interval.Interval class method) standardize_read() (mavis.validate.base.Evidence method) start (mavis.annotate.base.BioInterval attribute) START_AA (in module mavis.constants) start_splice_site (mavis.annotate.genomic.Exon attribute) stdev_count_abnormal stdev_fragment_size STOP_AA (in module mavis.constants) STRAND (in module mavis.constants) strand_determining_read stranded structural variant SummaryConfig (class in mavis.config) support() (mavis.validate.call.EventCall method) 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_diff() (in module mavis.main) to_dict() (mavis.annotate.base.BioInterval method) (mavis.annotate.genomic.Gene method) (mavis.annotate.genomic.IntergenicRegion method) (mavis.breakpoint.Breakpoint method) tools 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() (in module mavis.validate.call) 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)

U

union() (mavis.interval.Interval class method) unique_exists() (in module mavis.main) unspliced_transcript (mavis.annotate.genomic.Transcript attribute)

untemplated_seq update() (mavis.util.MavisNamespace method) usTranscript (class in mavis.annotate.genomic)

V

valid_chr() (mavis.bam.cache.BamCache method)

validate_and_cast_section() (in module mavis.config) validation_id

W

weighted_mean() (in module mavis.cluster.cluster)

write_bed_file() (in module mavis.util) write_config() (in module mavis.config)