Enum varlociraptor::cli::PreprocessKind
source · pub enum PreprocessKind {
Variants {Show 18 fields
reference: PathBuf,
candidates: PathBuf,
bam: PathBuf,
report_fragment_ids: bool,
atomic_candidate_variants: bool,
omit_mapq_adjustment: bool,
reference_buffer_size: usize,
min_bam_refetch_distance: u64,
alignment_properties: Option<PathBuf>,
output: Option<PathBuf>,
propagate_info_fields: Vec<String>,
protocol_strandedness: ProtocolStrandedness,
realignment_window: u64,
max_depth: usize,
omit_insert_size: bool,
pairhmm_mode: String,
log_mode: String,
output_raw_observations: Option<PathBuf>,
},
}
Variants§
Variants
Fields
§
protocol_strandedness: ProtocolStrandedness
Trait Implementations§
source§impl Clone for PreprocessKind
impl Clone for PreprocessKind
source§fn clone(&self) -> PreprocessKind
fn clone(&self) -> PreprocessKind
Returns a copy of the value. Read more
1.0.0 · source§fn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from
source
. Read moresource§impl Debug for PreprocessKind
impl Debug for PreprocessKind
source§impl<'de> Deserialize<'de> for PreprocessKind
impl<'de> Deserialize<'de> for PreprocessKind
source§fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
__D: Deserializer<'de>,
fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
__D: Deserializer<'de>,
Deserialize this value from the given Serde deserializer. Read more
source§impl Serialize for PreprocessKind
impl Serialize for PreprocessKind
source§impl StructOpt for PreprocessKind
impl StructOpt for PreprocessKind
source§fn from_clap(matches: &ArgMatches<'_>) -> Self
fn from_clap(matches: &ArgMatches<'_>) -> Self
Builds the struct from
clap::ArgMatches
. It’s guaranteed to succeed
if matches
originates from an App
generated by StructOpt::clap
called on
the same type, otherwise it must panic.source§fn from_args() -> Selfwhere
Self: Sized,
fn from_args() -> Selfwhere
Self: Sized,
Builds the struct from the command line arguments (
std::env::args_os
).
Calls clap::Error::exit
on failure, printing the error message and aborting the program.source§fn from_args_safe() -> Result<Self, Error>where
Self: Sized,
fn from_args_safe() -> Result<Self, Error>where
Self: Sized,
Builds the struct from the command line arguments (
std::env::args_os
).
Unlike StructOpt::from_args
, returns clap::Error
on failure instead of aborting the program,
so calling .exit
is up to you.source§fn from_iter<I>(iter: I) -> Self
fn from_iter<I>(iter: I) -> Self
Gets the struct from any iterator such as a
Vec
of your making.
Print the error message and quit the program in case of failure. Read moreAuto Trait Implementations§
impl RefUnwindSafe for PreprocessKind
impl Send for PreprocessKind
impl Sync for PreprocessKind
impl Unpin for PreprocessKind
impl UnwindSafe for PreprocessKind
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere
T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
§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>
The inverse inclusion map: attempts to construct
self
from the equivalent element of its
superset. Read more§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
Checks if
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
Use with care! Same as
self.to_subset
but without any property checks. Always succeeds.§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
The inclusion map: converts
self
to the equivalent element of its superset.