Bionano Scaffolding Correction Tool (BiSCOT)
Table of contents
Alignment module
Blat module
Key file related methods
Map module
General methods
Bionano Scaffolding Correction Tool (BiSCOT)
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Index
Index
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A
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B
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C
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E
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G
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L
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M
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P
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R
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S
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U
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W
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__init__() (biscot.Alignment.Alignment method)
(biscot.Map.Map method)
__str__() (biscot.Alignment.Alignment method)
(biscot.Map.Map method)
__weakref__ (biscot.Alignment.Alignment attribute)
(biscot.Map.Map attribute)
A
add_alignment() (biscot.Map.Map method)
add_channel_1_label() (biscot.Map.Map method)
add_channel_2_label() (biscot.Map.Map method)
agp_to_fasta() (in module biscot.Misc)
Alignment (class in biscot.Alignment)
B
biscot.Alignment (module)
biscot.Blat (module)
biscot.Key (module)
biscot.Map (module)
biscot.Misc (module)
blat_phase() (in module biscot.Blat)
C
check_containment() (biscot.Map.Map method)
check_map_containment() (in module biscot.Map)
check_path() (in module biscot.Misc)
E
extend_key_dict() (in module biscot.Key)
G
get_agp_changes() (in module biscot.Blat)
get_corresponding_contig_map_label() (biscot.Alignment.Alignment method)
get_label_position() (biscot.Map.Map method)
get_leftmost_label() (in module biscot.Alignment)
get_max_id() (in module biscot.Key)
get_rightmost_label() (in module biscot.Alignment)
get_shared_labels() (in module biscot.Alignment)
L
line_to_alignment() (in module biscot.Alignment)
load_contigs() (in module biscot.Misc)
M
Map (class in biscot.Map)
mute_agp_file() (in module biscot.Blat)
P
parse_blat() (in module biscot.Blat)
parse_contig_cmap() (in module biscot.Map)
parse_key() (in module biscot.Key)
parse_reference_cmap() (in module biscot.Map)
parse_xmap() (in module biscot.Alignment)
print() (in module biscot.Misc)
print_agp() (in module biscot.Alignment)
print_agp_line_no_intersection() (in module biscot.Alignment)
print_agp_line_with_intersection() (in module biscot.Alignment)
print_alignments() (biscot.Map.Map method)
print_gap_line() (in module biscot.Alignment)
R
run_blat() (in module biscot.Blat)
S
setup_logging() (in module biscot.Misc)
solve_alignment_containment() (in module biscot.Alignment)
solve_containment() (in module biscot.Alignment)
sort_alignments() (biscot.Map.Map method)
sort_map_alignments() (in module biscot.Map)
U
update_alignments() (biscot.Alignment.Alignment method)
W
write_new_agp() (in module biscot.Blat)
write_unplaced_contigs() (in module biscot.Alignment)