Index

A

add_contig_line() (vcfpy.Header method), [1] add_filter() (vcfpy.Record method), [1] add_filter_line() (vcfpy.Header method), [1] add_format() (vcfpy.Record method), [1] add_format_line() (vcfpy.Header method), [1] add_info_line() (vcfpy.Header method), [1]

add_line() (vcfpy.Header method), [1] affected_end (vcfpy.Record property), [1] affected_start (vcfpy.Record property), [1] ALT (vcfpy.Record attribute), [1] AltAlleleHeaderLine (class in vcfpy), [1] AltRecord (class in vcfpy), [1]

B

beg (vcfpy.tabix.Chunk attribute) begin (vcfpy.Record attribute), [1] BgzfReader (class in vcfpy.bgzf)

BgzfWriter (class in vcfpy.bgzf) Bin (class in vcfpy.tabix) bins (vcfpy.tabix.SequenceIndex attribute) BreakEnd (class in vcfpy), [1]

C

Call (class in vcfpy), [1] call_for_sample (vcfpy.Record attribute), [1] called (vcfpy.Call attribute), [1] calls (vcfpy.Record attribute), [1] CHROM (vcfpy.Record attribute), [1] Chunk (class in vcfpy.tabix) chunks (vcfpy.tabix.Bin attribute) close() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) (vcfpy.Reader method), [1] (vcfpy.tabix.TabixFile method) (vcfpy.Writer method), [1]

closed (vcfpy.bgzf.BgzfReader property) (vcfpy.bgzf.BgzfWriter property) col_beg (vcfpy.tabix.TabixIndex attribute) col_end (vcfpy.tabix.TabixIndex attribute) col_seq (vcfpy.tabix.TabixIndex attribute) CompoundHeaderLine (class in vcfpy), [1] ContigHeaderLine (class in vcfpy), [1] convert_field_value() (in module vcfpy.parser) copy() (vcfpy.CompoundHeaderLine method), [1] (vcfpy.Header method), [1] (vcfpy.HeaderLine method), [1] (vcfpy.SamplesInfos method), [1] (vcfpy.SimpleHeaderLine method), [1]

D

data (vcfpy.Call attribute), [1] description (vcfpy.FieldInfo attribute), [1] (vcfpy.FilterHeaderLine attribute), [1] (vcfpy.FormatHeaderLine attribute), [1] (vcfpy.InfoHeaderLine attribute), [1]

E

end (vcfpy.Record attribute), [1] (vcfpy.tabix.Chunk attribute)

F

fetch() (vcfpy.Reader method), [1] (vcfpy.tabix.TabixFile method) FieldInfo (class in vcfpy), [1] FileFormat (class in vcfpy.tabix) fileno() (vcfpy.bgzf.BgzfReader method) FILTER (vcfpy.Record attribute), [1] filter_ids() (vcfpy.Header method), [1] FilterHeaderLine (class in vcfpy), [1] flush() (vcfpy.bgzf.BgzfReader method) FORMAT (vcfpy.Record attribute), [1] format (vcfpy.tabix.TabixIndex attribute) format_ids() (vcfpy.Header method), [1]

FormatHeaderLine (class in vcfpy), [1] from_mapping() (vcfpy.AltAlleleHeaderLine class method), [1] (vcfpy.ContigHeaderLine class method), [1] (vcfpy.FilterHeaderLine class method), [1] (vcfpy.FormatHeaderLine class method), [1] (vcfpy.InfoHeaderLine class method), [1] (vcfpy.MetaHeaderLine class method), [1] (vcfpy.PedigreeHeaderLine class method), [1] (vcfpy.SampleHeaderLine class method), [1] from_path() (vcfpy.Reader class method), [1] (vcfpy.Writer class method), [1] from_stream() (vcfpy.Reader class method), [1] (vcfpy.Writer class method), [1]

G

GENERIC (vcfpy.tabix.FileFormat attribute) get_format_field_info() (vcfpy.Header method), [1] get_info_field_info() (vcfpy.Header method), [1] get_lines() (vcfpy.Header method), [1]

gt_alleles (vcfpy.Call attribute), [1] gt_bases (vcfpy.Call property), [1] gt_phase_char (vcfpy.Call property), [1] gt_type (vcfpy.Call property), [1]

H

has_header_line() (vcfpy.Header method), [1] Header (class in vcfpy), [1] header (vcfpy.parser.Parser attribute) (vcfpy.parser.RecordParser attribute) (vcfpy.Reader attribute), [1] (vcfpy.Writer attribute), [1]

header_without_lines() (in module vcfpy), [1] HeaderLine (class in vcfpy), [1] HeaderNotFound, [1] HeaderParser (class in vcfpy.parser)

I

id (vcfpy.AltAlleleHeaderLine attribute), [1] (vcfpy.ContigHeaderLine attribute), [1] (vcfpy.FieldInfo attribute), [1] (vcfpy.FilterHeaderLine attribute), [1] (vcfpy.FormatHeaderLine attribute), [1] (vcfpy.InfoHeaderLine attribute), [1] (vcfpy.MetaHeaderLine attribute), [1] (vcfpy.PedigreeHeaderLine attribute), [1] ID (vcfpy.Record attribute), [1] id (vcfpy.SampleHeaderLine attribute), [1] IncorrectVCFFormat, [1] indices (vcfpy.tabix.TabixIndex attribute)

INFO (vcfpy.Record attribute), [1] info_ids() (vcfpy.Header method), [1] InfoHeaderLine (class in vcfpy), [1] InvalidHeaderException, [1] InvalidRecordException, [1] is_filtered() (vcfpy.Call method), [1] is_het (vcfpy.Call property), [1] is_parsed() (vcfpy.SamplesInfos method), [1] is_phased (vcfpy.Call property), [1] is_snv() (vcfpy.Record method), [1] is_variant (vcfpy.Call property), [1] isatty() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method)

K

key (vcfpy.HeaderLine attribute), [1]

L

length (vcfpy.ContigHeaderLine attribute), [1]

lines (vcfpy.Header attribute), [1]

M

make_virtual_offset() (in module vcfpy.bgzf) mapping (vcfpy.CompoundHeaderLine attribute), [1] (vcfpy.SimpleHeaderLine attribute), [1] mate_chrom (vcfpy.BreakEnd attribute), [1] mate_orientation (vcfpy.BreakEnd attribute), [1] mate_pos (vcfpy.BreakEnd attribute), [1]

meta (vcfpy.tabix.TabixIndex attribute) MetaHeaderLine (class in vcfpy), [1] mode (vcfpy.bgzf.BgzfReader property) (vcfpy.bgzf.BgzfWriter property) module vcfpy vcfpy.version

N

name (vcfpy.bgzf.BgzfReader property) (vcfpy.bgzf.BgzfWriter property) name_to_idx (vcfpy.SamplesInfos attribute), [1]

names (vcfpy.SamplesInfos attribute), [1] num_no_coord (vcfpy.tabix.TabixIndex attribute) number (vcfpy.FieldInfo attribute), [1] (vcfpy.tabix.Bin attribute)

O

offsets (vcfpy.tabix.SequenceIndex attribute)

orientation (vcfpy.BreakEnd attribute), [1]

P

parse_field_value() (in module vcfpy.parser) parse_header() (vcfpy.parser.Parser method) parse_line() (vcfpy.parser.HeaderParser method) (vcfpy.parser.Parser method) (vcfpy.parser.RecordParser method) parse_next_record() (vcfpy.parser.Parser method) parsed_samples (vcfpy.Reader attribute), [1] (vcfpy.SamplesInfos attribute), [1]

Parser (class in vcfpy.parser) parser (vcfpy.Reader attribute), [1] path (vcfpy.Reader attribute), [1] (vcfpy.Writer attribute), [1] PedigreeHeaderLine (class in vcfpy), [1] ploidy (vcfpy.Call attribute), [1] POS (vcfpy.Record attribute), [1] print_warn_summary() (vcfpy.parser.Parser method)

Q

QUAL (vcfpy.Record attribute), [1]

R

read() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) read_index() (in module vcfpy.tabix) readable() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) Reader (class in vcfpy), [1] readline() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method)

readlines() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) Record (class in vcfpy), [1] record_checks (vcfpy.parser.Parser attribute) (vcfpy.parser.RecordParser attribute) (vcfpy.Reader attribute), [1] RecordParser (class in vcfpy.parser) REF (vcfpy.Record attribute), [1] reg2bins() (in module vcfpy.tabix)

S

SAM (vcfpy.tabix.FileFormat attribute) sample (vcfpy.Call attribute), [1] (vcfpy.UnparsedCall attribute) SampleHeaderLine (class in vcfpy), [1] samples (vcfpy.Header attribute), [1] (vcfpy.parser.Parser attribute) (vcfpy.parser.RecordParser attribute) SamplesInfos (class in vcfpy), [1] seek() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) seekable() (vcfpy.bgzf.BgzfReader method) sequence (vcfpy.BreakEnd attribute), [1] SequenceIndex (class in vcfpy.tabix) serialize() (vcfpy.AltRecord method), [1] (vcfpy.BreakEnd method), [1] (vcfpy.CompoundHeaderLine method), [1] (vcfpy.HeaderLine method), [1] (vcfpy.SimpleHeaderLine method), [1] (vcfpy.Substitution method), [1] (vcfpy.SymbolicAllele method), [1]

set_genotype() (vcfpy.Call method), [1] SimpleHeaderLine (class in vcfpy), [1] SingleBreakEnd (class in vcfpy), [1] site (vcfpy.Call attribute), [1] (vcfpy.UnparsedCall attribute) skip (vcfpy.tabix.TabixIndex attribute) source (vcfpy.FormatHeaderLine attribute), [1] (vcfpy.InfoHeaderLine attribute), [1] split_virtual_offset() (in module vcfpy.bgzf) stream (vcfpy.Reader attribute), [1] (vcfpy.Writer attribute), [1] sub_parsers (vcfpy.parser.HeaderParser attribute) Substitution (class in vcfpy), [1] SV (in module vcfpy) SymbolicAllele (class in vcfpy), [1]

T

tabix_file (vcfpy.Reader attribute), [1] tabix_path (vcfpy.Reader attribute), [1] TabixFile (class in vcfpy.tabix) TabixFileIter (class in vcfpy.tabix) TabixIndex (class in vcfpy.tabix) tell() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method)

truncate() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) type (vcfpy.AltRecord attribute), [1] (vcfpy.FieldInfo attribute), [1] (vcfpy.FormatHeaderLine attribute), [1] (vcfpy.InfoHeaderLine attribute), [1]

U

unparsed_data (vcfpy.UnparsedCall attribute)

UnparsedCall (class in vcfpy) update_calls() (vcfpy.Record method), [1]

V

value (vcfpy.CompoundHeaderLine property) (vcfpy.HeaderLine property) (vcfpy.SimpleHeaderLine property) (vcfpy.Substitution attribute), [1] (vcfpy.SymbolicAllele attribute), [1] VCF (vcfpy.tabix.FileFormat attribute)

vcfpy module vcfpy.version module VCFPyException, [1] version (vcfpy.FormatHeaderLine attribute), [1] (vcfpy.InfoHeaderLine attribute), [1]

W

within_main_assembly (vcfpy.BreakEnd attribute), [1] writable() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) write() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method)

write_record() (vcfpy.Writer method), [1] writelines() (vcfpy.bgzf.BgzfReader method) (vcfpy.bgzf.BgzfWriter method) Writer (class in vcfpy), [1]