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.interval.Interval method) __sub__() (mavis.interval.Interval method) __xor__() (mavis.interval.Interval method)

A

abs_dist() (mavis.cluster.cluster.IntervalPair static method) 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) 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_spanning_read() (mavis.validate.call.EventCall method) align_seq() (mavis.annotate.protein.Domain method)

alignment_matches() (in module mavis.bam.cigar) 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_remap assembly_strand_concordance

B

bam BamCache (class in mavis.bam.cache) BamStats (class in mavis.bam.stats) bed BioInterval (class in mavis.annotate.base) blat Blat (class in mavis.blat) blat_contigs() (in module mavis.blat) blat_min_identity blat_min_percent_of_max_score blat_min_query_consumption BlatAlignedSegment (class in mavis.blat) 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 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 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) build() (mavis.annotate.variant.FusionTranscript class method) build_batch_id() (in module mavis.pipeline.util)

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.pipeline.config) center (mavis.interval.Interval attribute) center_dist() (mavis.cluster.cluster.IntervalPair static method) chr (mavis.annotate.genomic.Gene attribute) (mavis.annotate.genomic.IntergenicRegion attribute) CIGAR (in module mavis.constants) classify() (mavis.breakpoint.BreakpointPair class method) close() (mavis.bam.cache.BamCache method) cluster() (mavis.cluster.cluster.IntervalPair class method) cluster_breakpoint_pairs() (in module mavis.cluster.cluster) 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_spanning_read() (mavis.validate.base.Evidence method) collect_split_read() (mavis.validate.base.Evidence method) COLUMNS (in module mavis.constants) 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_query_name contig_alignment_score contig_build_score 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_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) convert_ratioed_pos() (mavis.interval.Interval class method) copy() (mavis.breakpoint.BreakpointPair method) (mavis.validate.base.Evidence method)

D

DeBruijnGraph (class in mavis.assemble) decide_sequenced_strand() (mavis.validate.base.Evidence method) determine_prime() (in module mavis.annotate.variant) DiagramSettings (class in mavis.illustrate.constants) digraph_connected_components() (in module mavis.assemble) dist() (mavis.interval.Interval class method) 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_reads_bins fetch_reads_limit filter_on_overlap() (in module mavis.pipeline.util) filter_secondary_alignments flanking read pair 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.validate.base.Evidence method) (mavis.validate.call.EventCall method) 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_direction gene2 gene2_direction gene_product_type GENE_PRODUCT_TYPE (in module mavis.constants) 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) get_blat_version() (in module mavis.pipeline.util)

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_key() (mavis.illustrate.util.LabelMapping method) get_mate() (mavis.bam.cache.BamCache method) get_read_reference_name() (mavis.bam.cache.BamCache method) get_samtools_version() (in module mavis.pipeline.util) 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)

H

half-mapped read

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) IntervalPair (class in mavis.cluster.cluster) InvalidRearrangement is_complete() (in module mavis.cluster.cluster) items() (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)

kmers() (in module mavis.assemble)

L

LabelMapping (class in mavis.illustrate.util) length() (mavis.interval.Interval method) library linking_split_reads 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.pipeline.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.pairing.main) (in module mavis.validate.main) (in module mavis_run) main_pipeline() (in module mavis_run) match_percent() (in module mavis.bam.cigar) mavis (module), [1] mavis.annotate (module), [1] mavis.annotate.base (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.main (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.pairing (module), [1] mavis.pairing.main (module) mavis.pairing.pairing (module) mavis.pipeline (module), [1] mavis.pipeline.config (module) mavis.pipeline.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_run (module) max_expected_fragment_size (mavis.validate.base.Evidence attribute) max_sc_preceeding_anchor median() (mavis.bam.stats.Histogram method) median_fragment_size merge() (mavis.cluster.cluster.IntervalPair class method) merge_integer_intervals() (in module mavis.cluster.cluster) 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_resolutionraw_break1_half_mapped_reads 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.pipeline.util)

N

NA_MAPPING_QUALITY (in module mavis.constants)

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

P

paired_alignment_score() (in module mavis.blat) pairing parse_arguments() (in module mavis.pipeline.config) 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)

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

Q

query_coverage_interval() (mavis.blat.BlatAlignedSegment method)

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.pipeline.config) read_inputs() (in module mavis.pipeline.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.blat.BlatAlignedSegment attribute) remap_score() (mavis.assemble.Contig method) reverse_complement() (in module mavis.constants)

S

samtools_v0_sort() (in module mavis.validate.main) samtools_v1_sort() (in module mavis.validate.main) 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) 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_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_intervals_into_tracks() (in module mavis.illustrate.util) 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 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) 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 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_noncutting_paths_by_freq() (mavis.assemble.DeBruijnGraph method) trim_tails_by_freq() (mavis.assemble.DeBruijnGraph method)

U

union() (mavis.interval.Interval class method) unspliced_transcript (mavis.annotate.genomic.Transcript attribute)

untemplated_seq usTranscript (class in mavis.annotate.genomic)

V

validate_and_cast_section() (in module mavis.pipeline.config)

VALIDATION_DEFAULTS (in module mavis.validate.constants) validation_id

W

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

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