Struct varlociraptor::variants::evidence::observations::read_observation::ReadObservationBuilder
source · pub struct ReadObservationBuilder<P, A>where
P: Clone,
A: Clone,{ /* private fields */ }
Expand description
Builder for ReadObservation
.
Implementations§
source§impl<P, A> ReadObservationBuilder<P, A>where
P: Clone + Clone,
A: Clone + Clone,
impl<P, A> ReadObservationBuilder<P, A>where
P: Clone + Clone,
A: Clone + Clone,
pub fn name(&mut self, value: Option<String>) -> &mut Self
pub fn fragment_id(&mut self, value: Option<u64>) -> &mut Self
sourcepub fn prob_mapping(&mut self, value: LogProb) -> &mut Self
pub fn prob_mapping(&mut self, value: LogProb) -> &mut Self
Posterior probability that the read/read-pair has been mapped correctly (1 - MAPQ).
sourcepub fn prob_mismapping(&mut self, value: LogProb) -> &mut Self
pub fn prob_mismapping(&mut self, value: LogProb) -> &mut Self
Posterior probability that the read/read-pair has been mapped incorrectly (MAPQ).
sourcepub fn prob_alt(&mut self, value: LogProb) -> &mut Self
pub fn prob_alt(&mut self, value: LogProb) -> &mut Self
Probability that the read/read-pair comes from the alternative allele.
sourcepub fn prob_ref(&mut self, value: LogProb) -> &mut Self
pub fn prob_ref(&mut self, value: LogProb) -> &mut Self
Probability that the read/read-pair comes from the reference allele.
sourcepub fn prob_missed_allele(&mut self, value: LogProb) -> &mut Self
pub fn prob_missed_allele(&mut self, value: LogProb) -> &mut Self
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.
sourcepub fn prob_sample_alt(&mut self, value: LogProb) -> &mut Self
pub fn prob_sample_alt(&mut self, value: LogProb) -> &mut Self
Probability to sample the alt allele
pub fn prob_hit_base(&mut self, value: LogProb) -> &mut Self
sourcepub fn strand(&mut self, value: Strand) -> &mut Self
pub fn strand(&mut self, value: Strand) -> &mut Self
Strand evidence this observation relies on
sourcepub fn read_orientation(
&mut self,
value: SequenceReadPairOrientation
) -> &mut Self
pub fn read_orientation(
&mut self,
value: SequenceReadPairOrientation
) -> &mut Self
Read orientation support this observation relies on
sourcepub fn softclipped(&mut self, value: bool) -> &mut Self
pub fn softclipped(&mut self, value: bool) -> &mut Self
True if obervation contains s
pub fn paired(&mut self, value: bool) -> &mut Self
sourcepub fn read_position(&mut self, value: P) -> &mut Self
pub fn read_position(&mut self, value: P) -> &mut Self
Read position of the variant in the read (for SNV and MNV)
sourcepub fn prob_observable_at_homopolymer_artifact(
&mut self,
value: Option<LogProb>
) -> &mut Self
pub fn prob_observable_at_homopolymer_artifact(
&mut self,
value: Option<LogProb>
) -> &mut Self
Probability to make this observation at a homopolymer artifact
pub fn prob_observable_at_homopolymer_variant(
&mut self,
value: Option<LogProb>
) -> &mut Self
sourcepub fn homopolymer_indel_len(&mut self, value: Option<i8>) -> &mut Self
pub fn homopolymer_indel_len(&mut self, value: Option<i8>) -> &mut Self
Homopolymer indel length (None if there is no homopolymer indel compared to reference)
pub fn is_max_mapq(&mut self, value: bool) -> &mut Self
pub fn alt_locus(&mut self, value: A) -> &mut Self
sourcepub fn build(
&self
) -> Result<ReadObservation<P, A>, ReadObservationBuilderError>
pub fn build(
&self
) -> Result<ReadObservation<P, A>, ReadObservationBuilderError>
source§impl<P: Clone, A: Clone> ReadObservationBuilder<P, A>
impl<P: Clone, A: Clone> ReadObservationBuilder<P, A>
pub fn prob_mapping_mismapping(&mut self, prob_mapping: LogProb) -> &mut Self
pub fn prob_overlap(&mut self, prob_double_overlap: LogProb) -> &mut Self
Trait Implementations§
Auto Trait Implementations§
impl<P, A> RefUnwindSafe for ReadObservationBuilder<P, A>where
A: RefUnwindSafe,
P: RefUnwindSafe,
impl<P, A> Send for ReadObservationBuilder<P, A>where
A: Send,
P: Send,
impl<P, A> Sync for ReadObservationBuilder<P, A>where
A: Sync,
P: Sync,
impl<P, A> Unpin for ReadObservationBuilder<P, A>where
A: Unpin,
P: Unpin,
impl<P, A> UnwindSafe for ReadObservationBuilder<P, A>where
A: UnwindSafe,
P: UnwindSafe,
Blanket Implementations§
§impl<T> Pointable for T
impl<T> Pointable for T
§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
self
from the equivalent element of its
superset. Read more§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
self
is actually part of its subset T
(and can be converted to it).§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
self.to_subset
but without any property checks. Always succeeds.§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
self
to the equivalent element of its superset.