Struct varlociraptor::variants::evidence::observations::read_observation::ReadObservation
source · [−]pub struct ReadObservation<P = Option<u32>, A = ExactAltLoci> where
P: Clone,
A: Clone, {Show 18 fields
pub fragment_id: Option<u64>,
pub prob_alt: LogProb,
pub prob_ref: LogProb,
pub prob_missed_allele: LogProb,
pub prob_sample_alt: LogProb,
pub prob_double_overlap: LogProb,
pub prob_single_overlap: LogProb,
pub prob_hit_base: LogProb,
pub strand: Strand,
pub read_orientation: SequenceReadPairOrientation,
pub softclipped: bool,
pub paired: bool,
pub read_position: P,
pub prob_observable_at_homopolymer_artifact: Option<LogProb>,
pub prob_observable_at_homopolymer_variant: Option<LogProb>,
pub homopolymer_indel_len: Option<i8>,
pub is_max_mapq: bool,
pub alt_locus: A,
/* private fields */
}
Expand description
An observation for or against a variant.
Fields
fragment_id: Option<u64>
prob_alt: LogProb
Probability that the read/read-pair comes from the alternative allele.
prob_ref: LogProb
Probability that the read/read-pair comes from the reference allele.
prob_missed_allele: LogProb
Probability that the read/read-pair comes from an unknown allele at an unknown true locus (in case it is mismapped). This should usually be set as the product of the maxima of prob_ref and prob_alt per read.
prob_sample_alt: LogProb
Probability to sample the alt allele
prob_double_overlap: LogProb
Probability to overlap with both strands
prob_single_overlap: LogProb
Probability to overlap with one strand only (1-prob_double_overlap)
prob_hit_base: LogProb
strand: Strand
Strand evidence this observation relies on
read_orientation: SequenceReadPairOrientation
Read orientation support this observation relies on
softclipped: bool
True if obervation contains s
paired: bool
read_position: P
Read position of the variant in the read (for SNV and MNV)
prob_observable_at_homopolymer_artifact: Option<LogProb>
Probability to make this observation at a homopolymer artifact
prob_observable_at_homopolymer_variant: Option<LogProb>
homopolymer_indel_len: Option<i8>
Homopolymer indel length (None if there is no homopolymer indel compared to reference)
is_max_mapq: bool
alt_locus: A
Implementations
sourceimpl<P: Clone, A: Clone> ReadObservation<P, A>
impl<P: Clone, A: Clone> ReadObservation<P, A>
pub fn bayes_factor_alt(&self) -> BayesFactor
pub fn prob_mapping_orig(&self) -> LogProb
pub fn prob_mapping(&self) -> LogProb
pub fn prob_mismapping(&self) -> LogProb
pub fn is_uniquely_mapping(&self) -> bool
pub fn is_strong_alt_support(&self) -> bool
pub fn is_strong_ref_support(&self) -> bool
pub fn is_ref_support(&self) -> bool
pub fn is_positive_ref_support(&self) -> bool
pub fn has_homopolymer_error(&self) -> bool
Trait Implementations
sourceimpl<P: Clone, A: Clone> Clone for ReadObservation<P, A> where
P: Clone,
A: Clone,
impl<P: Clone, A: Clone> Clone for ReadObservation<P, A> where
P: Clone,
A: Clone,
sourcefn clone(&self) -> ReadObservation<P, A>
fn clone(&self) -> ReadObservation<P, A>
Returns a copy of the value. Read more
1.0.0 · sourcefn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from source
. Read more
Auto Trait Implementations
impl<P, A> RefUnwindSafe for ReadObservation<P, A> where
A: RefUnwindSafe,
P: RefUnwindSafe,
impl<P, A> Send for ReadObservation<P, A> where
A: Send,
P: Send,
impl<P, A> Sync for ReadObservation<P, A> where
A: Sync,
P: Sync,
impl<P, A> Unpin for ReadObservation<P, A> where
A: Unpin,
P: Unpin,
impl<P, A> UnwindSafe for ReadObservation<P, A> where
A: UnwindSafe,
P: UnwindSafe,
Blanket Implementations
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T: ?Sized,
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