Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | Q | R | S | T | V

A

add_filter() (vcfpy.record.Record method)
add_format() (vcfpy.record.Record method)
ALT (vcfpy.record.Record attribute)
AltRecord (class in vcfpy.record)

B

begin (vcfpy.record.Record attribute)
BND (in module vcfpy.record)
BreakEnd (class in vcfpy.record)

C

Call (class in vcfpy.record)
call_for_sample (vcfpy.record.Record attribute)
calls (vcfpy.record.Record attribute)
CHROM (vcfpy.record.Record attribute)
close() (vcfpy.reader.Reader method)
CompoundHeaderLine (class in vcfpy.header)
ContigHeaderLine (class in vcfpy.header)
convert_field_value() (in module vcfpy.parser)

D

data (vcfpy.record.Call attribute)
DEL (in module vcfpy.record)
description (vcfpy.header.FilterHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)

E

end (vcfpy.record.Record attribute)

F

FieldInfo (class in vcfpy.header)
FILTER (vcfpy.record.Record attribute)
FilterHeaderLine (class in vcfpy.header)
FORMAT (vcfpy.record.Record attribute)
FORMAT_TYPES (in module vcfpy.header)
FormatHeaderLine (class in vcfpy.header)
from_file() (vcfpy.reader.Reader class method)
from_path() (vcfpy.reader.Reader class method)

G

get_format_field_info() (vcfpy.header.Header method)
get_info_field_info() (vcfpy.header.Header method)
gt_bases (vcfpy.record.Call attribute)
gt_type (vcfpy.record.Call attribute)

H

Header (class in vcfpy.header)
header (vcfpy.parser.Parser attribute)
(vcfpy.parser.RecordParser attribute)
(vcfpy.reader.Reader attribute)
HEADER_NUMBER_ALLELES (in module vcfpy.header)
HEADER_NUMBER_GENOTYPES (in module vcfpy.header)
HEADER_NUMBER_REF (in module vcfpy.header)
HEADER_NUMBER_UNBOUNDED (in module vcfpy.header)
HeaderLine (class in vcfpy.header)
HeaderLineParserBase (class in vcfpy.parser)
HeaderNotFound
HeaderParser (class in vcfpy.parser)

I

id (vcfpy.header.ContigHeaderLine attribute)
(vcfpy.header.FilterHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
ID (vcfpy.record.Record attribute)
IncorrectVCFFormat
INDEL (in module vcfpy.record)
INFO (vcfpy.record.Record attribute)
INFO_TYPES (in module vcfpy.header)
InfoHeaderLine (class in vcfpy.header)
INS (in module vcfpy.record)
InvalidHeaderException
InvalidRecordException
is_filtered (vcfpy.record.Call attribute)
is_het (vcfpy.record.Call attribute)
is_phased (vcfpy.record.Call attribute)
is_variant (vcfpy.record.Call attribute)

J

jump_to() (vcfpy.reader.Reader method)

K

key (vcfpy.header.HeaderLine attribute)

L

length (vcfpy.header.ContigHeaderLine attribute)
line_class (vcfpy.parser.MappingHeaderLineParser attribute)
lines (vcfpy.header.Header attribute)
LINES_WITH_ID (in module vcfpy.header)

M

mapping (vcfpy.header.CompoundHeaderLine attribute)
(vcfpy.header.SimpleHeaderFile attribute)
MappingHeaderLineParser (class in vcfpy.parser)
MNV (in module vcfpy.record)

N

name_to_idx (vcfpy.header.SamplesInfos attribute)
names (vcfpy.header.SamplesInfos attribute)
number (vcfpy.header.FieldInfo attribute)

P

parse_field_value() (in module vcfpy.parser)
parse_header() (vcfpy.parser.Parser method)
parse_key_value() (vcfpy.parser.HeaderLineParserBase method)
(vcfpy.parser.MappingHeaderLineParser method)
(vcfpy.parser.StupidHeaderLineParser method)
parse_line() (vcfpy.parser.HeaderParser method)
(vcfpy.parser.Parser method)
(vcfpy.parser.RecordParser method)
parse_mapping() (in module vcfpy.parser)
parse_next_record() (vcfpy.parser.Parser method)
Parser (class in vcfpy.parser)
parser (vcfpy.reader.Reader attribute)
path (vcfpy.reader.Reader attribute)
POS (vcfpy.record.Record attribute)
process_alt() (in module vcfpy.parser)

Q

QUAL (vcfpy.record.Record attribute)

R

Reader (class in vcfpy.reader)
Record (class in vcfpy.record)
RecordParser (class in vcfpy.parser)
REF (vcfpy.record.Record attribute)

S

sample (vcfpy.record.Call attribute)
samples (vcfpy.header.Header attribute)
(vcfpy.parser.Parser attribute)
(vcfpy.parser.RecordParser attribute)
(vcfpy.reader.Reader attribute)
SamplesInfos (class in vcfpy.header)
serialize() (vcfpy.header.CompoundHeaderLine method)
(vcfpy.header.HeaderLine method)
(vcfpy.header.SimpleHeaderFile method)
serialize_for_header() (in module vcfpy.header)
SimpleHeaderFile (class in vcfpy.header)
SingleBreakEnd (class in vcfpy.record)
site (vcfpy.record.Call attribute)
SNV (in module vcfpy.record)
source (vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
split_quoted_string() (in module vcfpy.parser)
stream (vcfpy.reader.Reader attribute)
StupidHeaderLineParser (class in vcfpy.parser)
Substitution (class in vcfpy.record)
SUPPORTED_VCF_VERSIONS (in module vcfpy.parser)
SV (class in vcfpy.record)
SV_CODES (in module vcfpy.record)
SYMBOLIC (in module vcfpy.record)
SymbolicAllele (class in vcfpy.record)

T

tabix_file (vcfpy.reader.Reader attribute)
tabix_path (vcfpy.reader.Reader attribute)
type (vcfpy.header.FieldInfo attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
(vcfpy.record.AltRecord attribute)

V

VALID_NUMBERS (in module vcfpy.header)
value (vcfpy.header.HeaderLine attribute)
(vcfpy.record.BreakEnd attribute)
(vcfpy.record.SV attribute)
(vcfpy.record.SingleBreakEnd attribute)
(vcfpy.record.Substitution attribute)
(vcfpy.record.SymbolicAllele attribute)
vcfpy (module)
vcfpy.exceptions (module)
vcfpy.header (module)
vcfpy.parser (module)
vcfpy.reader (module)
vcfpy.record (module)
VCFPyException
version (vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)