MAVIS
v2.2.5
About
Inputs
Supported Dependencies
Running the Pipeline
Configuration and Settings
Resource Requirements
Theory and Models
Illustrations
Guidelines for Contributors
Package Documentation
Glossary
MAVIS
Docs
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Index
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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_arguments() (mavis.config.CustomHelpFormatter 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)
add_stranded_information() (mavis.bam.stats.BamStats method)
align_seq() (mavis.annotate.protein.Domain method)
align_sequences() (in module mavis.align)
aligner
,
[1]
aligner_reference
,
[1]
alignment_id() (mavis.align.SplitAlignment method)
(mavis.bam.read.SamRead method)
alignment_matches() (in module mavis.bam.cigar)
alignment_rank() (mavis.align.SplitAlignment method)
all_edges() (mavis.assemble.DeBruijnGraph method)
all_pair_group_keys() (in module mavis.cluster.cluster)
annotate_args() (in module mavis.schedule.pipeline)
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]
annotations
,
[1]
ArrayJob (class in mavis.schedule.job)
assemble() (in module mavis.assemble)
assemble_contig() (mavis.validate.base.Evidence method)
assembly_kmer_size
,
[1]
assembly_max_paths
,
[1]
assembly_min_edge_trim_weight
,
[1]
assembly_min_exact_match_to_remap
,
[1]
assembly_min_remap_coverage
,
[1]
assembly_min_remapped_seq
,
[1]
assembly_min_uniq
,
[1]
assembly_strand_concordance
,
[1]
augment_parser() (in module mavis.config)
B
BAM
bam_to_scatter() (in module mavis.illustrate.scatter)
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_read_names() (mavis.validate.call.EventCall method)
break1_split_reads
break1_split_reads_forced
break1_strand
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_read_names() (mavis.validate.call.EventCall method)
break2_split_reads
break2_split_reads_forced
break2_strand
BreakDancer
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)
BreakSeq
build() (mavis.annotate.fusion.FusionTranscript class method)
(mavis.config.LibraryConfig static method)
(mavis.schedule.pipeline.Pipeline class method)
BWA
C
CACHE (mavis.annotate.file_io.ReferenceFile attribute)
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)
call_sequence_complexity
cancel() (mavis.schedule.scheduler.Scheduler method)
(mavis.schedule.scheduler.SgeScheduler method)
(mavis.schedule.scheduler.SlurmScheduler method)
(mavis.schedule.scheduler.TorqueScheduler method)
cast() (in module mavis.util)
cdna_synon
center (mavis.interval.Interval attribute)
characterize_repeat_region() (mavis.validate.call.EventCall static method)
check_complete() (mavis.schedule.local.LocalJob method)
check_overlay_args() (in module mavis.main)
check_status() (mavis.schedule.pipeline.Pipeline method)
Chimerascan
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)
CIGAR (in module mavis.constants)
classify() (mavis.annotate.splicing.SplicingPattern class method)
(mavis.breakpoint.BreakpointPair class method)
clean_aligner_files
,
[1]
close() (mavis.bam.cache.BamCache method)
(mavis.schedule.local.LocalScheduler method)
cluster_args() (in module mavis.schedule.pipeline)
cluster_id
cluster_initial_size_limit
,
[1]
cluster_radius
,
[1]
cluster_size
CNVnator
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)
command() (mavis.schedule.scheduler.Scheduler method)
comparison_distance() (in module mavis.pairing.pairing)
compatible_type (mavis.validate.base.Evidence attribute)
COMPLETE_STAMP (in module mavis.constants)
complete_stamp() (mavis.schedule.job.ArrayJob method)
(mavis.schedule.job.Job method)
(mavis.schedule.job.Task method)
(mavis.schedule.job.TorqueArrayJob method)
complexity() (mavis.assemble.Contig method)
(mavis.validate.call.EventCall method)
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)
concurrency_limit
,
[1]
consecutive_ranges() (in module mavis.schedule.scheduler)
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)
(mavis.interval.IntervalMapping method)
convert_state() (mavis.schedule.scheduler.SgeScheduler class method)
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_from() (mavis.constants.MavisNamespace method)
copy_onto() (mavis.bam.read.SamRead class method)
copy_with_tasks() (mavis.schedule.job.ArrayJob method)
cterm_aligned (mavis.annotate.variant.IndelCall attribute)
cumulative_job_state() (in module mavis.schedule.constants)
CustomHelpFormatter (class in mavis.config)
D
DeBruijnGraph (class in mavis.assemble)
decide_sequenced_strand() (mavis.validate.base.Evidence method)
dedent() (mavis.util.Log 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.validate.constants)
define() (mavis.constants.MavisNamespace method)
DeFuse
del_seq (mavis.annotate.variant.IndelCall attribute)
deletion_sequences() (mavis.bam.read.SamRead method)
DELIM (mavis.constants.MavisNamespace attribute)
DELLY
determine_prime() (in module mavis.annotate.fusion)
dgv_annotation
,
[1]
DiagramSettings (class in mavis.illustrate.constants)
digraph_connected_components() (in module mavis.assemble)
discard() (mavis.constants.MavisNamespace method)
DISEASE_STATUS (in module mavis.constants)
display_name (mavis.schedule.job.Job attribute)
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)
ENV_ARRAY_IDENT (mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.SlurmScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
ENV_JOB_IDENT (mavis.schedule.scheduler.Scheduler attribute)
(mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.SlurmScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
ENV_JOB_NAME (mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
ENV_TASK_IDENT (mavis.schedule.scheduler.Scheduler attribute)
(mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.SlurmScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
equivalent() (in module mavis.pairing.pairing)
ERROR_STATES (mavis.schedule.pipeline.Pipeline attribute)
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_min_focus_size
,
[1]
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]
filepath() (in module mavis.util)
files_exist() (mavis.annotate.file_io.ReferenceFile method)
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_complexity
,
[1]
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_trans_homopolymers
,
[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.schedule.job.ArrayJob method)
(mavis.schedule.job.Job method)
(mavis.schedule.local.LocalJob 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)
format_args() (mavis.schedule.pipeline.Pipeline class method)
format_dependencies() (mavis.schedule.scheduler.Scheduler method)
(mavis.schedule.scheduler.SgeScheduler method)
(mavis.schedule.scheduler.SlurmScheduler method)
(mavis.schedule.scheduler.TorqueScheduler method)
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_aligner_version() (in module mavis.align)
get_bed_repesentation() (mavis.breakpoint.BreakpointPair method)
(mavis.validate.base.Evidence method)
(mavis.validate.call.EventCall method)
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_connected_components() (in module mavis.util)
get_edge_freq() (mavis.assemble.DeBruijnGraph method)
get_env_name() (mavis.constants.MavisNamespace method)
get_env_var() (mavis.constants.MavisNamespace 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_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_task() (mavis.schedule.job.ArrayJob method)
get_xml() (mavis.illustrate.util.Tag method)
GIEMSA_STAIN (in module mavis.constants)
group_by_distance() (in module mavis.summary.summary)
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_task() (mavis.schedule.job.ArrayJob method)
has_transcriptome() (mavis.config.MavisConfig method)
HEADER_PREFIX (mavis.schedule.scheduler.Scheduler attribute)
(mavis.schedule.scheduler.SgeScheduler attribute)
HGVS
hgvs_protein_notation() (mavis.annotate.variant.IndelCall method)
hgvs_standardize_cigar() (in module mavis.bam.cigar)
Histogram (class in mavis.bam.stats)
HOMOPOLYMER_MIN_LENGTH (in module mavis.summary.constants)
I
IGV
IGV batch file
import_env
,
[1]
IndelCall (class in mavis.annotate.variant)
indent() (mavis.util.Log method)
inferred_equivalent() (in module mavis.pairing.pairing)
inferred_pairing
input_call_distance
,
[1]
ins_seq (mavis.annotate.variant.IndelCall attribute)
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_dup (mavis.annotate.variant.IndelCall attribute)
is_empty() (mavis.annotate.file_io.ReferenceFile method)
is_env_overwritable() (mavis.constants.MavisNamespace method)
(mavis.util.WeakMavisNamespace method)
is_listable() (mavis.constants.MavisNamespace method)
is_loaded() (mavis.annotate.file_io.ReferenceFile method)
is_nullable() (mavis.constants.MavisNamespace method)
is_putative_indel (mavis.breakpoint.BreakpointPair attribute)
is_reverse (mavis.annotate.base.BioInterval attribute)
is_supplementary() (mavis.validate.call.EventCall method)
is_trans() (mavis.config.LibraryConfig method)
items() (mavis.constants.MavisNamespace method)
(mavis.illustrate.util.LabelMapping method)
J
Job (class in mavis.schedule.job)
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)
(mavis.bam.read.SamRead method)
keys() (mavis.constants.MavisNamespace method)
(mavis.interval.IntervalMapping 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)
limit_to_chr
,
[1]
linking_split_read_names() (mavis.validate.call.EventCall method)
linking_split_reads
load() (mavis.annotate.file_io.ReferenceFile method)
load_annotations() (in module mavis.annotate.file_io)
load_evidence() (mavis.validate.base.Evidence method)
LOAD_FUNCTIONS (mavis.annotate.file_io.ReferenceFile attribute)
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)
LocalJob (class in mavis.schedule.local)
LocalScheduler (class in mavis.schedule.local)
Log (class in mavis.util)
log_arguments() (in module mavis.util)
LogFile (class in mavis.schedule.job)
logfile() (mavis.schedule.job.ArrayJob method)
(mavis.schedule.job.Job method)
(mavis.schedule.job.Task method)
(mavis.schedule.job.TorqueArrayJob method)
longest_exact_match() (in module mavis.bam.cigar)
longest_fuzzy_match() (in module mavis.bam.cigar)
M
mail_type
,
[1]
MAIL_TYPE (in module mavis.schedule.constants)
MAIL_TYPE_MAPPING (mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
mail_user
,
[1]
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)
Manta
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]
masking
,
[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.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.schedule (module)
,
[1]
mavis.schedule.constants (module)
mavis.schedule.job (module)
mavis.schedule.local (module)
mavis.schedule.pipeline (module)
mavis.schedule.scheduler (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_call_complexity
,
[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)
mut_seq (mavis.annotate.variant.IndelCall attribute)
N
NA_MAPPING_QUALITY (in module mavis.constants)
NAME (mavis.schedule.local.LocalScheduler attribute)
(mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.SlurmScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
nameable_string() (in module mavis.config)
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)
nterm_aligned (mavis.annotate.variant.IndelCall attribute)
NullableType (class in mavis.util)
O
opposing_strands
OPTIONS (in module mavis.schedule.constants)
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_by_distance() (in module mavis.pairing.pairing)
pair_key() (in module mavis.cluster.cluster)
pairing
parse() (mavis.schedule.job.LogFile class method)
parse_annotations_json() (in module mavis.annotate.file_io)
parse_args() (mavis.config.LibraryConfig class method)
parse_listable_string() (mavis.constants.MavisNamespace class method)
parse_qacct() (mavis.schedule.scheduler.SgeScheduler class method)
parse_qstat() (mavis.schedule.scheduler.SgeScheduler class method)
(mavis.schedule.scheduler.TorqueScheduler class method)
parse_run_time() (in module mavis.schedule.pipeline)
parse_sacct() (mavis.schedule.scheduler.SlurmScheduler class method)
parse_scontrol_show() (mavis.schedule.scheduler.SlurmScheduler class method)
percent_identity() (mavis.blat.Blat static method)
pileup() (in module mavis.bam.read)
Pindel
Pipeline (class in mavis.schedule.pipeline)
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
product_key() (in module mavis.pairing.pairing)
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_breakpoint() (in module mavis.align)
read_build_file() (mavis.schedule.pipeline.Pipeline class method)
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)
ref_seq (mavis.annotate.variant.IndelCall attribute)
reference_genome
,
[1]
reference_id() (mavis.bam.cache.BamCache method)
reference_name (mavis.bam.read.SamRead attribute)
ReferenceFile (class in mavis.annotate.file_io)
ReferenceName (class in mavis.annotate.base)
remap_coverage() (mavis.assemble.Contig method)
remap_depth() (mavis.assemble.Contig method)
remap_score() (mavis.assemble.Contig method)
remote_head_ssh
,
[1]
remove_task() (mavis.schedule.job.ArrayJob method)
reset() (mavis.schedule.job.ArrayJob method)
(mavis.schedule.job.Job method)
(mavis.schedule.job.Task method)
reverse() (mavis.constants.MavisNamespace method)
reverse_complement() (in module mavis.constants)
run_conversion() (in module mavis.schedule.pipeline)
S
SamRead (class in mavis.bam.read)
scaffold_color
,
[1]
ScatterPlot (class in mavis.illustrate.scatter)
scheduler
,
[1]
Scheduler (class in mavis.schedule.scheduler)
SCHEDULER (in module mavis.schedule.constants)
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)
sequence_complexity() (in module mavis.bam.read)
sequenced_strand() (in module mavis.bam.read)
set_key() (mavis.bam.read.SamRead method)
(mavis.illustrate.util.LabelMapping method)
SGE
SgeScheduler (class in mavis.schedule.scheduler)
single_transcript() (mavis.annotate.variant.Annotation method)
SLURM
SlurmScheduler (class in mavis.schedule.scheduler)
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)
STAR-Fusion
start (mavis.annotate.base.BioInterval attribute)
START_AA (in module mavis.constants)
STATE_MAPPING (mavis.schedule.scheduler.SgeScheduler attribute)
(mavis.schedule.scheduler.TorqueScheduler attribute)
STATUS (mavis.schedule.job.LogFile attribute)
stdev_count_abnormal
,
[1]
STOP_AA (in module mavis.constants)
STRAND (in module mavis.constants)
strand_determining_read
,
[1]
stranded
Strelka
stringify_args_to_command() (in module mavis.schedule.pipeline)
structural variant
SUBCOMMAND (in module mavis.constants)
submit() (mavis.schedule.local.LocalScheduler method)
(mavis.schedule.scheduler.Scheduler method)
(mavis.schedule.scheduler.SgeScheduler method)
(mavis.schedule.scheduler.SlurmScheduler method)
(mavis.schedule.scheduler.TorqueScheduler method)
summary_args() (in module mavis.schedule.pipeline)
supplementary_call
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)
SV
SVG
SVTYPE (in module mavis.constants)
T
TAB_SIZE (mavis.schedule.scheduler.TorqueScheduler attribute)
Tag (class in mavis.illustrate.util)
Task (class in mavis.schedule.job)
tasks (mavis.schedule.job.ArrayJob attribute)
Template (class in mavis.annotate.genomic)
template_metadata
,
[1]
terminates (mavis.annotate.variant.IndelCall attribute)
time_format() (in module mavis.schedule.scheduler)
time_limit
,
[1]
to_dict() (mavis.annotate.base.BioInterval method)
(mavis.annotate.genomic.Gene method)
(mavis.annotate.genomic.IntergenicRegion method)
(mavis.breakpoint.Breakpoint method)
(mavis.constants.MavisNamespace method)
tools
TORQUE
TorqueArrayJob (class in mavis.schedule.job)
TorqueScheduler (class in mavis.schedule.scheduler)
tracking_id
Trans-ABySS
trans_fetch_reads_limit
,
[1]
trans_min_mapping_quality
,
[1]
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
untemplated_shift() (mavis.breakpoint.BreakpointPair method)
update_info() (mavis.schedule.local.LocalScheduler method)
(mavis.schedule.scheduler.Scheduler method)
(mavis.schedule.scheduler.SgeScheduler method)
(mavis.schedule.scheduler.SlurmScheduler method)
(mavis.schedule.scheduler.TorqueScheduler method)
V
valid_chr() (mavis.bam.cache.BamCache method)
validate_args() (in module mavis.schedule.pipeline)
validate_section() (in module mavis.config)
validation_id
validation_memory
,
[1]
values() (mavis.constants.MavisNamespace method)
W
wait() (mavis.schedule.local.LocalScheduler method)
(mavis.schedule.scheduler.Scheduler method)
WeakMavisNamespace (class in mavis.util)
weighted_mean() (in module mavis.cluster.cluster)
width
,
[1]
write_bed_file() (in module mavis.util)
write_build_file() (mavis.schedule.pipeline.Pipeline method)
write_config() (in module mavis.config)
write_evidence_files
,
[1]
write_stamp_callback() (in module mavis.schedule.local)
write_submission_script() (mavis.schedule.pipeline.Pipeline method)
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