Enum noodles_vcf::header::info::key::Standard

pub enum Standard {
    AncestralAllele,
    AlleleCount,
    TotalReadDepths,
    ForwardStrandReadDepths,
    ReverseStrandReadDepths,
    AlleleFrequencies,
    TotalAlleleCount,
    BaseQuality,
    Cigar,
    IsInDbSnp,
    TotalDepth,
    IsInHapMap2,
    IsInHapMap3,
    MappingQuality,
    ZeroMappingQualityCount,
    SamplesWithDataCount,
    StrandBias,
    IsSomaticMutation,
    IsValidated,
    IsIn1000Genomes,
    IsImprecise,
    IsNovel,
    EndPosition,
    SvType,
    SvLengths,
    PositionConfidenceIntervals,
    EndConfidenceIntervals,
    MicrohomologyLengths,
    MicrohomologySequences,
    BreakpointIds,
    MobileElementInfo,
    MobileElementTransductionInfo,
    DbvId,
    DbVarId,
    DbRipId,
    MateBreakendIds,
    PartnerBreakendId,
    BreakendEventId,
    EventType,
    BreakendConfidenceIntervals,
    AdjacentReadDepths,
    BreakendCopyNumber,
    AdjacentCopyNumber,
    CopyNumberConfidenceIntervals,
    AdjacentCopyNumberConfidenceIntervals,
    SvClaim,
    TotalRepeatSequenceCounts,
    RepeatUnitSequences,
    RepeatUnitLengths,
    RepeatUnitCounts,
    TotalRepeatSequenceBaseCounts,
    RepeatUnitCountConfidenceIntervals,
    TotalRepeatSequenceBaseCountConfidenceIntervals,
    RepeatUnitBaseCounts,
}

A VCF header info key.

Variants

AncestralAllele

Ancestral allele (AA).

AlleleCount

Allele count in genotypes, for each ALT allele, in the same order as listed (AC).

TotalReadDepths

Total read depth for each allele (AD).

ForwardStrandReadDepths

Read depth for each allele on the forward strand (ADF).

ReverseStrandReadDepths

Read depth for each allele on the reverse strand (ADR).

AlleleFrequencies

Allele frequency for each ALT allele in the same order as listed (AF).

TotalAlleleCount

Total number of alleles in called genotypes (AN).

BaseQuality

RMS base quality (BQ).

Cigar

Cigar string describing how to align an alternate allele to the reference allele (CIGAR).

IsInDbSnp

dbSNP membership (DB).

TotalDepth

Combined depth across samples (DP).

IsInHapMap2

HapMap2 membership (H2).

IsInHapMap3

HapMap3 membership (H3).

MappingQuality

RMS mapping quality (MQ).

ZeroMappingQualityCount

Number of MAPQ == 0 reads (MQ0).

SamplesWithDataCount

Number of samples with data (NS).

StrandBias

Strand bias (SB).

IsSomaticMutation

Somatic mutation (SOMATIC).

IsValidated

Validated by follow-up experiment (VALIDATED).

IsIn1000Genomes

1000 Genomes membership (1000G).

IsImprecise

Imprecise structural variation (IMPRECISE).

IsNovel

Indicates a novel structural variation (NOVEL).

EndPosition

End position of the variant described in this record (END).

SvType

Type of structural variant (SVTYPE).

Deprecated in VCF 4.4.

SvLengths

Difference in length between REF and ALT alleles (SVLEN).

PositionConfidenceIntervals

Confidence interval around POS for imprecise variants (CIPOS).

EndConfidenceIntervals

Confidence interval around END for imprecise variants (CIEND).

MicrohomologyLengths

Length of base pair identical micro-homology at event breakpoints (HOMLEN).

MicrohomologySequences

Sequence of base pair identical micro-homology at event breakpoints (HOMSEQ).

BreakpointIds

ID of the assembled alternate allele in the assembly file (BKPTID).

MobileElementInfo

Mobile element info of the form NAME,START,END,POLARITY (MEINFO).

MobileElementTransductionInfo

Mobile element transduction info of the form CHR,START,END,POLARITY (METRANS).

DbvId

ID of this element in Database of Genomic Variation (DBVID).

DbVarId

ID of this element in DBVAR (DBVARID).

DbRipId

ID of this element in DBRIP (DBRIPID).

MateBreakendIds

ID of mate breakends (MATEID).

PartnerBreakendId

ID of partner breakend (PARID).

BreakendEventId

ID of event associated to breakend (EVENT).

EventType

ID of associated event (EVENTTYPE).

Added in VCF 4.4.

BreakendConfidenceIntervals

Confidence interval around the inserted material between breakends (CILEN).

AdjacentReadDepths

Read Depth of adjacency (DPADJ).

Deprecated in VCF 4.4.

BreakendCopyNumber

Copy number of segment containing breakend (CN).

AdjacentCopyNumber

Copy number of adjacency (CNADJ).

Deprecated in VCF 4.4.

CopyNumberConfidenceIntervals

Confidence interval around copy number for the segment (CICN).

AdjacentCopyNumberConfidenceIntervals

Confidence interval around copy number for the adjacency (CICNADJ).

Deprecated in VCF 4.4.

SvClaim

Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively.

Added in VCF 4.4.

TotalRepeatSequenceCounts

Total number of repeat sequences in this allele (RN).

Added in VCF 4.4.

RepeatUnitSequences

Repeat unit sequence of the corresponding repeat sequence (RUS).

Added in VCF 4.4.

RepeatUnitLengths

Repeat unit length of the corresponding repeat sequence (RUL).

Added in VCF 4.4.

RepeatUnitCounts

Repeat unit count of corresponding repeat sequence (RUC).

Added in VCF 4.4.

TotalRepeatSequenceBaseCounts

Total number of bases in the corresponding repeat sequence (RB).

Added in VCF 4.4.

RepeatUnitCountConfidenceIntervals

Confidence interval around RUC (CIRUC).

Added in VCF 4.4.

TotalRepeatSequenceBaseCountConfidenceIntervals

Confidence interval around RB (CIRB).

Added in VCF 4.4.

RepeatUnitBaseCounts

Number of bases in each individual repeat unit (RUB).

Added in VCF 4.4.

Trait Implementations

impl AsRef<str> for Standard

fn as_ref(&self) -> &str

Converts this type into a shared reference of the (usually inferred) input type.

impl Clone for Standard

fn clone(&self) -> Standard

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Standard

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromStr for Standard

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl Hash for Standard

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl PartialEq<Standard> for Standard

fn eq(&self, other: &Standard) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Copy for Standard

impl Eq for Standard

impl StructuralEq for Standard

impl StructuralPartialEq for Standard