pub struct FastQCConfig {Show 20 fields
pub nogroup: bool,
pub expgroup: bool,
pub quiet: bool,
pub kmer_size: u8,
pub threads: usize,
pub output_dir: Option<PathBuf>,
pub casava: bool,
pub nano: bool,
pub nofilter: bool,
pub do_unzip: Option<bool>,
pub delete_after_unzip: bool,
pub sequence_format: Option<String>,
pub contaminant_file: Option<PathBuf>,
pub adapter_file: Option<PathBuf>,
pub limits_file: Option<PathBuf>,
pub min_length: usize,
pub dup_length: usize,
pub svg_output: bool,
pub temp_dir: Option<PathBuf>,
pub template: TemplateName,
}Expand description
Configuration for a FastQC run, mirroring all fields from Java FastQCConfig.
Fields§
§nogroup: bool§expgroup: bool§quiet: bool§kmer_size: u8§threads: usize§output_dir: Option<PathBuf>§casava: bool§nano: bool§nofilter: bool§do_unzip: Option<bool>§delete_after_unzip: bool§sequence_format: Option<String>§contaminant_file: Option<PathBuf>§adapter_file: Option<PathBuf>§limits_file: Option<PathBuf>§min_length: usize§dup_length: usize§svg_output: bool§temp_dir: Option<PathBuf>§template: TemplateNameImplementations§
Source§impl FastQCConfig
impl FastQCConfig
Sourcepub fn load_limits(&self) -> Result<Limits>
pub fn load_limits(&self) -> Result<Limits>
Load module limits from the configured file or the embedded default.
Parsing matches ModuleConfig.java - lines starting with ‘#’
are comments, blank lines are skipped, and each data line has whitespace-
separated fields: module level value.
Sourcepub fn load_adapters(&self) -> Result<Vec<(String, String)>>
pub fn load_adapters(&self) -> Result<Vec<(String, String)>>
Load adapter sequences from the configured file or the embedded default.
Returns a list of (name, sequence) pairs.
Parsing matches the Java adapter loading - lines starting with ‘#’ are comments, blank lines are skipped, and each data line is tab- delimited with name and sequence columns.
Trait Implementations§
Source§impl Clone for FastQCConfig
impl Clone for FastQCConfig
Source§fn clone(&self) -> FastQCConfig
fn clone(&self) -> FastQCConfig
Returns a duplicate 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 FastQCConfig
impl Debug for FastQCConfig
Auto Trait Implementations§
impl Freeze for FastQCConfig
impl RefUnwindSafe for FastQCConfig
impl Send for FastQCConfig
impl Sync for FastQCConfig
impl Unpin for FastQCConfig
impl UnsafeUnpin for FastQCConfig
impl UnwindSafe for FastQCConfig
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
Source§impl<T> CloneToUninit for Twhere
T: Clone,
impl<T> CloneToUninit for Twhere
T: Clone,
Source§impl<T> IntoEither for T
impl<T> IntoEither for T
Source§fn into_either(self, into_left: bool) -> Either<Self, Self>
fn into_either(self, into_left: bool) -> Either<Self, Self>
Converts
self into a Left variant of Either<Self, Self>
if into_left is true.
Converts self into a Right variant of Either<Self, Self>
otherwise. Read moreSource§fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
Converts
self into a Left variant of Either<Self, Self>
if into_left(&self) returns true.
Converts self into a Right variant of Either<Self, Self>
otherwise. Read moreSource§impl<T> Pointable for T
impl<T> Pointable for T
Source§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
Source§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 moreSource§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).Source§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.Source§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
The inclusion map: converts
self to the equivalent element of its superset.