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vcfpy
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B
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C
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D
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E
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F
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
add_contig_line() (vcfpy.Header method)
(vcfpy.header.Header method)
add_filter() (vcfpy.Record method)
(vcfpy.record.Record method)
add_filter_line() (vcfpy.Header method)
(vcfpy.header.Header method)
add_format() (vcfpy.Record method)
(vcfpy.record.Record method)
add_format_line() (vcfpy.Header method)
(vcfpy.header.Header method)
add_info_line() (vcfpy.Header method)
(vcfpy.header.Header method)
add_line() (vcfpy.Header method)
(vcfpy.header.Header method)
affected_end (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
affected_start (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
ALLELE_DELIM (in module vcfpy.record)
ALT (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
AltAlleleHeaderLine (class in vcfpy)
(class in vcfpy.header)
AltRecord (class in vcfpy)
(class in vcfpy.record)
ARRAY (vcfpy.parser.QuotedStringSplitter attribute)
B
begin (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
BgzfWriter (class in vcfpy.bgzf)
binomial (in module vcfpy.parser)
BND (in module vcfpy.record)
BreakEnd (class in vcfpy)
(class in vcfpy.record)
build_header_parsers() (in module vcfpy.parser)
C
Call (class in vcfpy)
(class in vcfpy.record)
call_for_sample (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
called (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
calls (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
CannotConvertValue
CHROM (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
clear() (vcfpy.OrderedDict method)
close() (vcfpy.bgzf.BgzfWriter method)
(vcfpy.Reader method)
(vcfpy.Writer method)
(vcfpy.reader.Reader method)
(vcfpy.writer.Writer method)
CompoundHeaderLine (class in vcfpy)
(class in vcfpy.header)
ContigHeaderLine (class in vcfpy)
(class in vcfpy.header)
convert_field_value() (in module vcfpy.parser)
copy() (vcfpy.CompoundHeaderLine method)
(vcfpy.Header method)
(vcfpy.HeaderLine method)
(vcfpy.OrderedDict method)
(vcfpy.SamplesInfos method)
(vcfpy.SimpleHeaderLine method)
(vcfpy.header.CompoundHeaderLine method)
(vcfpy.header.Header method)
(vcfpy.header.HeaderLine method)
(vcfpy.header.SamplesInfos method)
(vcfpy.header.SimpleHeaderLine method)
D
data (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
DEL (in module vcfpy.record)
DELIM (vcfpy.parser.QuotedStringSplitter attribute)
delim (vcfpy.parser.QuotedStringSplitter attribute)
description (vcfpy.FieldInfo attribute)
(vcfpy.FilterHeaderLine attribute)
(vcfpy.FormatHeaderLine attribute)
(vcfpy.InfoHeaderLine attribute)
(vcfpy.header.FieldInfo attribute)
(vcfpy.header.FilterHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
DuplicateHeaderLineWarning
E
end (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
ESCAPE_MAPPING (in module vcfpy.record)
ESCAPED (vcfpy.parser.QuotedStringSplitter attribute)
F
fetch() (vcfpy.Reader method)
(vcfpy.reader.Reader method)
FieldInfo (class in vcfpy)
(class in vcfpy.header)
FieldInfoNotFound
FieldInvalidNumber
FieldMissingNumber
fileno() (vcfpy.bgzf.BgzfWriter method)
FILTER (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
filter_ids() (vcfpy.Header method)
(vcfpy.header.Header method)
FilterHeaderLine (class in vcfpy)
(class in vcfpy.header)
FIVE_PRIME (in module vcfpy.record)
flush() (vcfpy.bgzf.BgzfWriter method)
FORMAT (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
format_atomic() (in module vcfpy.writer)
format_ids() (vcfpy.Header method)
(vcfpy.header.Header method)
FORMAT_TYPES (in module vcfpy.header)
format_value() (in module vcfpy.writer)
FormatChecker (class in vcfpy.parser)
FormatHeaderLine (class in vcfpy)
(class in vcfpy.header)
FORWARD (in module vcfpy.record)
from_mapping() (vcfpy.AltAlleleHeaderLine class method)
(vcfpy.ContigHeaderLine class method)
(vcfpy.FilterHeaderLine class method)
(vcfpy.FormatHeaderLine class method)
(vcfpy.InfoHeaderLine class method)
(vcfpy.MetaHeaderLine class method)
(vcfpy.PedigreeHeaderLine class method)
(vcfpy.SampleHeaderLine class method)
(vcfpy.header.AltAlleleHeaderLine class method)
(vcfpy.header.ContigHeaderLine class method)
(vcfpy.header.FilterHeaderLine class method)
(vcfpy.header.FormatHeaderLine class method)
(vcfpy.header.InfoHeaderLine class method)
(vcfpy.header.MetaHeaderLine class method)
(vcfpy.header.PedigreeHeaderLine class method)
(vcfpy.header.SampleHeaderLine class method)
from_path() (vcfpy.Reader class method)
(vcfpy.Writer class method)
(vcfpy.reader.Reader class method)
(vcfpy.writer.Writer class method)
from_stream() (vcfpy.Reader class method)
(vcfpy.Writer class method)
(vcfpy.reader.Reader class method)
(vcfpy.writer.Writer class method)
fromkeys() (vcfpy.OrderedDict method)
G
get_format_field_info() (vcfpy.Header method)
(vcfpy.header.Header method)
get_info_field_info() (vcfpy.Header method)
(vcfpy.header.Header method)
get_lines() (vcfpy.Header method)
(vcfpy.header.Header method)
gt_alleles (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
gt_bases (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
gt_phase_char (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
gt_type (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
H
has_header_line() (vcfpy.Header method)
(vcfpy.header.Header method)
Header (class in vcfpy)
(class in vcfpy.header)
header (vcfpy.parser.FormatChecker attribute)
(vcfpy.Reader attribute)
(vcfpy.Writer attribute)
(vcfpy.parser.InfoChecker attribute)
(vcfpy.parser.Parser attribute)
(vcfpy.parser.RecordParser attribute)
(vcfpy.reader.Reader attribute)
(vcfpy.writer.Writer 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)
header_without_lines() (in module vcfpy)
(in module vcfpy.header)
HeaderChecker (class in vcfpy.parser)
HeaderInvalidType
HeaderLine (class in vcfpy)
(class in vcfpy.header)
HeaderLineParserBase (class in vcfpy.parser)
HeaderMissingDescription
HeaderNotFound
,
[1]
HeaderParser (class in vcfpy.parser)
HET (in module vcfpy.record)
HOM_ALT (in module vcfpy.record)
HOM_REF (in module vcfpy.record)
I
id (vcfpy.AltAlleleHeaderLine attribute)
(vcfpy.ContigHeaderLine attribute)
(vcfpy.FieldInfo attribute)
(vcfpy.FilterHeaderLine attribute)
(vcfpy.FormatHeaderLine attribute)
(vcfpy.InfoHeaderLine attribute)
(vcfpy.MetaHeaderLine attribute)
(vcfpy.PedigreeHeaderLine attribute)
(vcfpy.header.AltAlleleHeaderLine attribute)
(vcfpy.header.ContigHeaderLine attribute)
(vcfpy.header.FieldInfo attribute)
(vcfpy.header.FilterHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
(vcfpy.header.MetaHeaderLine attribute)
(vcfpy.header.PedigreeHeaderLine attribute)
(vcfpy.header.SampleHeaderLine attribute)
ID (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
id (vcfpy.SampleHeaderLine attribute)
IncorrectListLength
IncorrectVCFFormat
,
[1]
INDEL (in module vcfpy.record)
INFO (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
info_ids() (vcfpy.Header method)
(vcfpy.header.Header method)
INFO_TYPES (in module vcfpy.header)
InfoChecker (class in vcfpy.parser)
InfoHeaderLine (class in vcfpy)
(class in vcfpy.header)
INS (in module vcfpy.record)
InvalidHeaderException
,
[1]
InvalidRecordException
,
[1]
is_filtered() (vcfpy.Call method)
(vcfpy.record.Call method)
is_het (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
is_parsed() (vcfpy.header.SamplesInfos method)
(vcfpy.SamplesInfos method)
is_phased (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
is_snv() (vcfpy.Record method)
(vcfpy.record.Record method)
is_variant (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
isatty() (vcfpy.bgzf.BgzfWriter class method)
K
key (vcfpy.header.HeaderLine attribute)
(vcfpy.HeaderLine attribute)
L
LeadingTrailingSpaceInKey
length (vcfpy.ContigHeaderLine attribute)
(vcfpy.header.ContigHeaderLine attribute)
line_class (vcfpy.parser.MappingHeaderLineParser attribute)
lines (vcfpy.Header attribute)
(vcfpy.header.Header attribute)
LINES_WITH_ID (in module vcfpy.header)
M
make_virtual_offset() (in module vcfpy.bgzf)
mapping (vcfpy.CompoundHeaderLine attribute)
(vcfpy.SimpleHeaderLine attribute)
(vcfpy.header.CompoundHeaderLine attribute)
(vcfpy.header.SimpleHeaderLine attribute)
mapping_to_str() (in module vcfpy.header)
MappingHeaderLineParser (class in vcfpy.parser)
mate_chrom (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
mate_orientation (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
mate_pos (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
MetaHeaderLine (class in vcfpy)
(class in vcfpy.header)
MIXED (in module vcfpy.record)
MNV (in module vcfpy.record)
move_to_end() (vcfpy.OrderedDict method)
N
name_to_idx (vcfpy.header.SamplesInfos attribute)
(vcfpy.SamplesInfos attribute)
names (vcfpy.header.SamplesInfos attribute)
(vcfpy.SamplesInfos attribute)
NoopFormatChecker (class in vcfpy.parser)
NoopInfoChecker (class in vcfpy.parser)
NORMAL (vcfpy.parser.QuotedStringSplitter attribute)
number (vcfpy.FieldInfo attribute)
(vcfpy.header.FieldInfo attribute)
O
OrderedDict (class in vcfpy)
orientation (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
P
parse_breakend() (in module vcfpy.parser)
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)
parsed_samples (vcfpy.header.SamplesInfos attribute)
(vcfpy.Reader attribute)
(vcfpy.SamplesInfos attribute)
(vcfpy.reader.Reader attribute)
Parser (class in vcfpy.parser)
parser (vcfpy.Reader attribute)
(vcfpy.reader.Reader attribute)
path (vcfpy.Reader attribute)
(vcfpy.Writer attribute)
(vcfpy.reader.Reader attribute)
(vcfpy.writer.Writer attribute)
PedigreeHeaderLine (class in vcfpy)
(class in vcfpy.header)
plodity (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
pop() (vcfpy.OrderedDict method)
popitem() (vcfpy.OrderedDict method)
POS (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
print_warn_summary() (vcfpy.parser.Parser method)
process_alt() (in module vcfpy.parser)
process_sub() (in module vcfpy.parser)
process_sub_grow() (in module vcfpy.parser)
process_sub_shrink() (in module vcfpy.parser)
Q
QUAL (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
quote (vcfpy.parser.QuotedStringSplitter attribute)
QUOTED (vcfpy.parser.QuotedStringSplitter attribute)
QuotedStringSplitter (class in vcfpy.parser)
R
Reader (class in vcfpy)
(class in vcfpy.reader)
Record (class in vcfpy)
(class in vcfpy.record)
record_checks (vcfpy.parser.Parser attribute)
(vcfpy.Reader attribute)
(vcfpy.parser.RecordParser attribute)
(vcfpy.reader.Reader attribute)
RecordParser (class in vcfpy.parser)
REF (vcfpy.Record attribute)
(vcfpy.record.Record attribute)
RESERVED_CHARS (in module vcfpy.record)
RESERVED_INFO (in module vcfpy.header)
REVERSE (in module vcfpy.record)
run() (vcfpy.parser.FormatChecker method)
(vcfpy.parser.HeaderChecker method)
(vcfpy.parser.InfoChecker method)
(vcfpy.parser.NoopFormatChecker method)
(vcfpy.parser.NoopInfoChecker method)
(vcfpy.parser.QuotedStringSplitter method)
S
sample (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
(vcfpy.record.UnparsedCall attribute)
SampleHeaderLine (class in vcfpy)
(class in vcfpy.header)
samples (vcfpy.Header attribute)
(vcfpy.header.Header attribute)
(vcfpy.parser.Parser attribute)
(vcfpy.parser.RecordParser attribute)
SamplesInfos (class in vcfpy)
(class in vcfpy.header)
seekable() (vcfpy.bgzf.BgzfWriter method)
sequence (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
serialize() (vcfpy.AltRecord method)
(vcfpy.BreakEnd method)
(vcfpy.HeaderLine method)
(vcfpy.header.CompoundHeaderLine method)
(vcfpy.header.HeaderLine method)
(vcfpy.header.SimpleHeaderLine method)
(vcfpy.record.AltRecord method)
(vcfpy.record.BreakEnd method)
(vcfpy.record.Substitution method)
(vcfpy.record.SymbolicAllele method)
serialize_for_header() (in module vcfpy.header)
setdefault() (vcfpy.OrderedDict method)
SimpleHeaderLine (class in vcfpy)
(class in vcfpy.header)
SingleBreakEnd (class in vcfpy)
(class in vcfpy.record)
site (vcfpy.Call attribute)
(vcfpy.record.Call attribute)
(vcfpy.record.UnparsedCall attribute)
SNV (in module vcfpy.record)
source (vcfpy.FormatHeaderLine attribute)
(vcfpy.InfoHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
SpaceInChromLine
split_mapping() (in module vcfpy.parser)
split_quoted_string() (in module vcfpy.parser)
stream (vcfpy.Reader attribute)
(vcfpy.Writer attribute)
(vcfpy.reader.Reader attribute)
(vcfpy.writer.Writer attribute)
StupidHeaderLineParser (class in vcfpy.parser)
sub_parsers (vcfpy.parser.HeaderParser attribute)
Substitution (class in vcfpy)
(class in vcfpy.record)
SUPPORTED_VCF_VERSIONS (in module vcfpy.parser)
SV (in module vcfpy)
(in module vcfpy.record)
SYMBOLIC (in module vcfpy.record)
SymbolicAllele (class in vcfpy)
(class in vcfpy.record)
T
tabix_file (vcfpy.Reader attribute)
(vcfpy.reader.Reader attribute)
tabix_path (vcfpy.Reader attribute)
(vcfpy.reader.Reader attribute)
tell() (vcfpy.bgzf.BgzfWriter method)
THREE_PRIME (in module vcfpy.record)
type (vcfpy.AltRecord attribute)
(vcfpy.FieldInfo attribute)
(vcfpy.FormatHeaderLine attribute)
(vcfpy.InfoHeaderLine attribute)
(vcfpy.header.FieldInfo attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
(vcfpy.record.AltRecord attribute)
U
UNESCAPE_MAPPING (in module vcfpy.record)
UnknownFilter
UnknownVCFVersion
unparsed_data (vcfpy.record.UnparsedCall attribute)
UnparsedCall (class in vcfpy.record)
V
VALID_NUMBERS (in module vcfpy.header)
value (vcfpy.header.CompoundHeaderLine attribute)
(vcfpy.Substitution attribute)
(vcfpy.SymbolicAllele attribute)
(vcfpy.header.HeaderLine attribute)
(vcfpy.header.SimpleHeaderLine attribute)
(vcfpy.record.Substitution attribute)
(vcfpy.record.SymbolicAllele attribute)
vcfpy (module)
vcfpy.bgzf (module)
vcfpy.exceptions (module)
vcfpy.header (module)
vcfpy.parser (module)
vcfpy.reader (module)
vcfpy.record (module)
vcfpy.writer (module)
VCFPyException
,
[1]
VCFPyWarning
version (vcfpy.FormatHeaderLine attribute)
(vcfpy.InfoHeaderLine attribute)
(vcfpy.header.FormatHeaderLine attribute)
(vcfpy.header.InfoHeaderLine attribute)
W
within_main_assembly (vcfpy.BreakEnd attribute)
(vcfpy.record.BreakEnd attribute)
write() (vcfpy.bgzf.BgzfWriter method)
write_record() (vcfpy.Writer method)
(vcfpy.writer.Writer method)
Writer (class in vcfpy)
(class in vcfpy.writer)
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