Index

_ | A | B | C | D | E | F | G | H | I | M | N | O | P | R | S | T | V | W

_

_AltRecord (class in vcf.model)
_Breakend (class in vcf.parser)
_Call (class in vcf.model)
_Record (class in vcf.model)
_SingleBreakend (class in vcf.model)
_Substitution (class in vcf.model)
_SV (class in vcf.model)

A

aaf (vcf.model._Record attribute)
affected_end (vcf.model._Record attribute)
affected_start (vcf.model._Record attribute)
alleles (vcf.model._Record attribute)
alts (vcf.Reader attribute)
AvgDepthPerSample (class in vcf.filters)

B

Base (class in vcf.filters)

C

call_rate (vcf.model._Record attribute)
close() (vcf.Writer method)
connectingSequence (vcf.parser._Breakend attribute)
contigs (vcf.Reader attribute)
customize_parser() (vcf.filters.Base class method)

D

data (vcf.model._Call attribute)
DepthPerSample (class in vcf.filters)

E

end (vcf.model._Record attribute)
ErrorBiasFilter (class in vcf.filters)

F

fetch() (vcf.Reader method)
filter_name() (vcf.filters.Base method)
filters (vcf.Reader attribute)
flush() (vcf.Writer method)
formats (vcf.Reader attribute)

G

genotype() (vcf.model._Record method)
get_hets() (vcf.model._Record method)
get_hom_alts() (vcf.model._Record method)
get_hom_refs() (vcf.model._Record method)
get_unknowns() (vcf.model._Record method)
gt_bases (vcf.model._Call attribute)
gt_type (vcf.model._Call attribute)

H

heterozygosity (vcf.model._Record attribute)

I

infos (vcf.Reader attribute)
is_deletion (vcf.model._Record attribute)
is_filtered (vcf.model._Call attribute)
(vcf.model._Record attribute)
is_het (vcf.model._Call attribute)
is_indel (vcf.model._Record attribute)
is_monomorphic (vcf.model._Record attribute)
is_snp (vcf.model._Record attribute)
is_sv (vcf.model._Record attribute)
is_sv_precise (vcf.model._Record attribute)
is_transition (vcf.model._Record attribute)
is_variant (vcf.model._Call attribute)

M

metadata (vcf.Reader attribute)

N

name (vcf.filters.Base attribute)
next() (vcf.Reader method)
nucl_diversity (vcf.model._Record attribute)
num_called (vcf.model._Record attribute)
num_het (vcf.model._Record attribute)
num_hom_alt (vcf.model._Record attribute)
num_hom_ref (vcf.model._Record attribute)
num_unknown (vcf.model._Record attribute)

O

orientation (vcf.parser._Breakend attribute)

P

phased (vcf.model._Call attribute)
POS (vcf.model._Record attribute)

R

Reader (class in vcf)
remoteOrientation (vcf.parser._Breakend attribute)

S

sample (vcf.model._Call attribute)
samples (vcf.model._Record attribute)
sequence (vcf.model._Substitution attribute)
site (vcf.model._Call attribute)
SiteQuality (class in vcf.filters)
SnpOnly (class in vcf.filters)
start (vcf.model._Record attribute)
sv_end (vcf.model._Record attribute)

T

trim_common_suffix() (in module vcf.utils)
type (vcf.model._AltRecord attribute)

V

var_subtype (vcf.model._Record attribute)
var_type (vcf.model._Record attribute)
VariantGenotypeQuality (class in vcf.filters)
vcf.utils (module)

W

walk_together() (in module vcf.utils)
withinMainAssembly (vcf.parser._Breakend attribute)
write_record() (vcf.Writer method)
Writer (class in vcf)