Index

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.VCFReader method) convert_field_value() (in module vcfpy.parser)

D

data (vcfpy.record.Call attribute) DEL (in module vcfpy.record)

description (vcfpy.header.VCFFilterHeaderLine attribute) (vcfpy.header.VCFFormatHeaderLine attribute) (vcfpy.header.VCFInfoHeaderLine attribute)

E

end (vcfpy.record.Record attribute)

F

FieldInfo (class in vcfpy.header) FILTER (vcfpy.record.Record attribute) FORMAT (vcfpy.record.Record attribute)

FORMAT_TYPES (in module vcfpy.header) from_file() (vcfpy.reader.VCFReader class method) from_path() (vcfpy.reader.VCFReader class method)

G

get_format_field_info() (vcfpy.header.VCFHeader method) get_info_field_info() (vcfpy.header.VCFHeader method)

gt_bases (vcfpy.record.Call attribute) gt_type (vcfpy.record.Call attribute)

H

header (vcfpy.parser.VCFParser attribute) (vcfpy.parser.VCFRecordParser attribute) (vcfpy.reader.VCFReader 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) HeaderNotFound

I

id (vcfpy.header.VCFContigHeaderLine attribute) (vcfpy.header.VCFFilterHeaderLine attribute) (vcfpy.header.VCFFormatHeaderLine attribute) (vcfpy.header.VCFInfoHeaderLine attribute) ID (vcfpy.record.Record attribute) IncorrectVCFFormat INDEL (in module vcfpy.record) INFO (vcfpy.record.Record attribute) INFO_TYPES (in module 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.VCFReader method)

K

key (vcfpy.header.VCFHeaderLine attribute)

L

length (vcfpy.header.VCFContigHeaderLine attribute) line_class (vcfpy.parser.MappingVCFHeaderLineParser attribute)

lines (vcfpy.header.VCFHeader attribute) LINES_WITH_ID (in module vcfpy.header)

M

mapping (vcfpy.header.VCFCompoundHeaderLine attribute) (vcfpy.header.VCFSimpleHeaderLine attribute) MappingVCFHeaderLineParser (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.VCFParser method) parse_key_value() (vcfpy.parser.MappingVCFHeaderLineParser method) (vcfpy.parser.StupidVCFHeaderLineParser method) (vcfpy.parser.VCFHeaderLineParserBase method) parse_line() (vcfpy.parser.VCFHeaderParser method) (vcfpy.parser.VCFRecordParser method) parse_mapping() (in module vcfpy.parser)

parse_next_record() (vcfpy.parser.VCFParser method) parser (vcfpy.reader.VCFReader attribute) path (vcfpy.reader.VCFReader attribute) POS (vcfpy.record.Record attribute) process_alt() (in module vcfpy.parser)

Q

QUAL (vcfpy.record.Record attribute)

R

Record (class in vcfpy.record)

REF (vcfpy.record.Record attribute)

S

sample (vcfpy.record.Call attribute) samples (vcfpy.header.VCFHeader attribute) (vcfpy.parser.VCFParser attribute) (vcfpy.parser.VCFRecordParser attribute) (vcfpy.reader.VCFReader attribute) SamplesInfos (class in vcfpy.header) serialize() (vcfpy.header.VCFCompoundHeaderLine method) (vcfpy.header.VCFHeaderLine method) (vcfpy.header.VCFSimpleHeaderLine method) serialize_for_header() (in module vcfpy.header) SingleBreakEnd (class in vcfpy.record) site (vcfpy.record.Call attribute) SNV (in module vcfpy.record) source (vcfpy.header.VCFFormatHeaderLine attribute) (vcfpy.header.VCFInfoHeaderLine attribute)

split_quoted_string() (in module vcfpy.parser) stream (vcfpy.reader.VCFReader attribute) StupidVCFHeaderLineParser (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

type (vcfpy.header.FieldInfo attribute) (vcfpy.header.VCFFormatHeaderLine attribute) (vcfpy.header.VCFInfoHeaderLine attribute) (vcfpy.record.AltRecord attribute)

V

VALID_NUMBERS (in module vcfpy.header) value (vcfpy.header.VCFHeaderLine attribute) (vcfpy.record.BreakEnd attribute) (vcfpy.record.SV attribute) (vcfpy.record.SingleBreakEnd attribute) (vcfpy.record.Substitution attribute) (vcfpy.record.SymbolicAllele attribute) VCFCompoundHeaderLine (class in vcfpy.header) VCFContigHeaderLine (class in vcfpy.header) VCFFilterHeaderLine (class in vcfpy.header) VCFFormatHeaderLine (class in vcfpy.header) VCFHeader (class in vcfpy.header) VCFHeaderLine (class in vcfpy.header) VCFHeaderLineParserBase (class in vcfpy.parser) VCFHeaderParser (class in vcfpy.parser) VCFInfoHeaderLine (class in vcfpy.header) VCFParser (class in vcfpy.parser)

vcfpy (module) vcfpy.exceptions (module) vcfpy.header (module) vcfpy.parser (module) vcfpy.reader (module) vcfpy.record (module) VCFPyException VCFReader (class in vcfpy.reader) VCFRecordParser (class in vcfpy.parser) VCFSimpleHeaderLine (class in vcfpy.header) version (vcfpy.header.VCFFormatHeaderLine attribute) (vcfpy.header.VCFInfoHeaderLine attribute)