Index

A

add() (generate_cnv_graph.ConnectedComponent method)

add_edge() (generate_cnv_graph.Vertex method)

B

bed (module)

C

check_profiles() (in module generate_cnv_graph) clean() (in module parsers.breakdancer) clean_ccs() (in module generate_cnv_graph) cnv (class in cnv_struct) cnv_counter (module) cnv_db (module) cnv_db.db (module) cnv_generator() (generate_cnv_graph.ConnectedComponent method) cnv_struct (module)

compare_dgv (module) ConnectedComponent (class in generate_cnv_graph) create_db() (in module samples_db) create_dgv() (in module cnv_db.db) create_family_graph() (in module generate_cnv_graph) create_label() (in module venn) create_seek_index() (in module generate_cnv_graph) create_venn_from_dict() (in module venn)

D

de_novo_germinal (module)

E

Edge (class in generate_cnv_graph)

F

family_intersection() (in module cnv_struct) family_to_list() (in module parsers)

family_union() (in module cnv_struct)

G

generate_cnv_graph (module) get_cnvs() (parsers.ParentParser method) get_coverage() (in module generate_cnv_graph) get_coverage_for_sample() (in module samples_db) get_inherited() (in module mendelian)

get_parser_for_algorithm() (in module parsers) get_parser_if_valid() (in module validation) get_pos() (cnv_struct.cnv method) get_sample_ids_for_family() (in module samples_db)

M

main() (in module bed) (in module cnv_counter) (in module compare_dgv) (in module de_novo_germinal) (in module generate_cnv_graph) (in module mendelian) (in module merge_cnvs) (in module plot_cnv_size_dgv_ro) (in module plot_cnv_size_distribution) (in module plot_distance_distribution) (in module plot_ro) (in module plot_size_doc_scatter) mendelian (module) merge() (in module merge_cnvs)

merge_ccs() (in module generate_cnv_graph) merge_cnvs (module) merge_cnvs() (in module cnv_struct)

N

normalize_attributes() (cnv_struct.cnv method)

normalize_pileups_starting_position() (in module generate_cnv_graph)

O

overlap() (in module cnv_struct)

P

ParentParser (class in parsers) Parser (class in parsers.breakdancer) (class in parsers.cnver) (class in parsers.cnvnator) (class in parsers.cnvpickle) (class in parsers.erds) (class in parsers.omni25) parsers (module) parsers.breakdancer (module) parsers.cnver (module) parsers.cnvnator (module) parsers.cnvpickle (module) parsers.erds (module) parsers.omni25 (module)

plot_cnv_size_dgv_ro (module) plot_cnv_size_distribution (module) plot_distance_distribution (module) plot_in_same_plot() (in module plot_size_doc_scatter) plot_in_subplots() (in module plot_size_doc_scatter) plot_ro (module) plot_size_doc_scatter (module) position_based_venn() (in module venn)

Q

query_dgv_overlap() (in module cnv_db.db)

R

remove() (generate_cnv_graph.ConnectedComponent method)

ro_to_best_in_list() (in module cnv_struct)

S

samples_db (module) seek_to() (in module generate_cnv_graph)

suitable() (generate_cnv_graph.ConnectedComponent method)

V

validation (module) venn (module)

Vertex (class in generate_cnv_graph)

W

write_bed() (in module merge_cnvs) write_beds() (in module bed)

write_pickle() (in module merge_cnvs)