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D
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F
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I
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K
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M
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S
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T
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V
A
ambig_equal() (genomvar.variant.AmbigDel method)
(genomvar.variant.AmbigIndel method)
(genomvar.variant.AmbigIns method)
(genomvar.variant.Del method)
(genomvar.variant.Indel method)
(genomvar.variant.Ins method)
AmbigDel (class in genomvar.variant)
AmbigIndel (class in genomvar.variant)
AmbigIns (class in genomvar.variant)
Asterisk (class in genomvar.variant)
B
BCFReader (class in genomvar.vcf)
C
chroms() (genomvar.varset.VariantSet property)
(genomvar.varset.VariantSetFromFile property)
CmpSet (class in genomvar.varset)
comm() (genomvar.varset.VariantSet method)
comm_vrt() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
copy() (genomvar.varset.VariantSet method)
count() (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC method)
ctg_len (genomvar.varset.VariantSet attribute)
D
Del (class in genomvar.variant)
DESCRIPTION (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
diff() (genomvar.varset.VariantSet method)
diff_vrt() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
drop_duplicates() (genomvar.varset.VariantSet method)
E
edit_equal() (genomvar.variant.AmbigDel method)
(genomvar.variant.AmbigIndel method)
(genomvar.variant.AmbigIns method)
(genomvar.variant.Asterisk method)
(genomvar.variant.Del method)
(genomvar.variant.GenomVariant method)
(genomvar.variant.Haplotype method)
(genomvar.variant.Indel method)
(genomvar.variant.Ins method)
(genomvar.variant.Mixed method)
(genomvar.variant.MNP method)
(genomvar.variant.Null method)
(genomvar.variant.SNP method)
(genomvar.variant.VariantBase method)
F
file (genomvar.varset.VariantSetFromFile attribute)
find_rows() (genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
find_vrt() (genomvar.variant.Haplotype method)
(genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
(genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
from_edit() (genomvar.variant.VariantFactory method)
from_hgvs() (genomvar.variant.VariantFactory method)
from_variants() (genomvar.variant.Haplotype class method)
(genomvar.varset.VariantSet class method)
from_vcf() (genomvar.varset.VariantSet class method)
G
genomvar.variant
module
genomvar.varset
module
,
[1]
genomvar.vcf
module
genomvar.vcf_utils
module
GenomVariant (class in genomvar.variant)
get_chroms() (genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
get_factory() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
(genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
get_records() (genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
get_row() (genomvar.vcf.VCFWriter method)
H
Haplotype (class in genomvar.variant)
I
Indel (class in genomvar.variant)
index() (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC method)
Ins (class in genomvar.variant)
is_variant_instance() (genomvar.variant.AmbigDel method)
(genomvar.variant.AmbigIndel method)
(genomvar.variant.AmbigIns method)
(genomvar.variant.Asterisk method)
(genomvar.variant.Del method)
(genomvar.variant.Haplotype method)
(genomvar.variant.Indel method)
(genomvar.variant.Ins method)
(genomvar.variant.Mixed method)
(genomvar.variant.MNP method)
(genomvar.variant.Null method)
(genomvar.variant.SNP method)
(genomvar.variant.VariantBase method)
is_variant_subclass() (genomvar.variant.AmbigDel class method)
(genomvar.variant.AmbigIndel class method)
(genomvar.variant.AmbigIns class method)
(genomvar.variant.Asterisk class method)
(genomvar.variant.Del class method)
(genomvar.variant.Haplotype class method)
(genomvar.variant.Indel class method)
(genomvar.variant.Ins class method)
(genomvar.variant.Mixed class method)
(genomvar.variant.MNP class method)
(genomvar.variant.Null class method)
(genomvar.variant.SNP class method)
(genomvar.variant.VariantBase class method)
issequence() (in module genomvar.vcf_utils)
iter_rows() (genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
iter_rows_by_chrom() (genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
iter_vrt() (genomvar.varset.CmpSet method)
(genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
(genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
iter_vrt_by_chrom() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
(genomvar.vcf.BCFReader method)
(genomvar.vcf.VCFReader method)
K
key() (genomvar.variant.AmbigDel property)
(genomvar.variant.AmbigIndel property)
(genomvar.variant.AmbigIns property)
(genomvar.variant.Asterisk property)
(genomvar.variant.Del property)
(genomvar.variant.Haplotype property)
(genomvar.variant.Indel property)
(genomvar.variant.Ins property)
(genomvar.variant.Mixed property)
(genomvar.variant.MNP property)
(genomvar.variant.Null property)
(genomvar.variant.SNP property)
(genomvar.variant.VariantBase property)
M
match() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
Mixed (class in genomvar.variant)
MNP (class in genomvar.variant)
module
genomvar.variant
genomvar.varset
,
[1]
genomvar.vcf
genomvar.vcf_utils
N
NAME (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
nof_unit_vrt() (genomvar.varset.VariantSet method)
Null (class in genomvar.variant)
NUMBER (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
O
ovlp() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
R
reference (genomvar.varset.VariantSet attribute)
region() (genomvar.varset.CmpSet method)
S
sample() (genomvar.varset.VariantSet method)
seq() (genomvar.variant.AmbigDel property)
(genomvar.variant.AmbigIns property)
SNP (class in genomvar.variant)
sort_chroms() (genomvar.varset.VariantSet method)
SOURCE (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
T
to_records() (genomvar.varset.VariantSet method)
to_vcf() (genomvar.varset.VariantSet method)
(genomvar.varset.VariantSetFromFile method)
TYPE (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
V
VariantBase (class in genomvar.variant)
VariantFactory (class in genomvar.variant)
VariantSet (class in genomvar.varset)
VariantSetFromFile (class in genomvar.varset)
VCF_INFO_OR_FORMAT_SPEC (class in genomvar.vcf_utils)
VCFReader (class in genomvar.vcf)
VCFRow (class in genomvar.vcf_utils)
VCFWriter (class in genomvar.vcf)
VERSION (genomvar.vcf_utils.VCF_INFO_OR_FORMAT_SPEC attribute)
vtp() (genomvar.variant.AmbigDel property)
(genomvar.variant.AmbigIndel property)
(genomvar.variant.AmbigIns property)
(genomvar.variant.Asterisk property)
(genomvar.variant.Del property)
(genomvar.variant.Haplotype property)
(genomvar.variant.Indel property)
(genomvar.variant.Ins property)
(genomvar.variant.Mixed property)
(genomvar.variant.MNP property)
(genomvar.variant.Null property)
(genomvar.variant.SNP property)
(genomvar.variant.VariantBase property)
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