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Config

bbnorm_rs::cli

Struct Config 

Source 
pub struct Config {
Show 164 fields
    pub in1: Option<PathBuf>,
    pub in2: Option<PathBuf>,
    pub extra: Vec<PathBuf>,
    pub out1: Option<PathBuf>,
    pub out2: Option<PathBuf>,
    pub out_toss1: Option<PathBuf>,
    pub out_toss2: Option<PathBuf>,
    pub out_low1: Option<PathBuf>,
    pub out_low2: Option<PathBuf>,
    pub out_mid1: Option<PathBuf>,
    pub out_mid2: Option<PathBuf>,
    pub out_high1: Option<PathBuf>,
    pub out_high2: Option<PathBuf>,
    pub out_uncorrected1: Option<PathBuf>,
    pub out_uncorrected2: Option<PathBuf>,
    pub hist_in: Option<PathBuf>,
    pub hist_out: Option<PathBuf>,
    pub rhist_in: Option<PathBuf>,
    pub rhist_out: Option<PathBuf>,
    pub peaks_in: Option<PathBuf>,
    pub peaks_out: Option<PathBuf>,
    pub match_hist_out: Option<PathBuf>,
    pub insert_hist_out: Option<PathBuf>,
    pub quality_accuracy_hist_out: Option<PathBuf>,
    pub indel_hist_out: Option<PathBuf>,
    pub error_hist_out: Option<PathBuf>,
    pub quality_hist_out: Option<PathBuf>,
    pub base_quality_hist_out: Option<PathBuf>,
    pub quality_count_hist_out: Option<PathBuf>,
    pub average_quality_hist_out: Option<PathBuf>,
    pub overall_base_quality_hist_out: Option<PathBuf>,
    pub length_hist_out: Option<PathBuf>,
    pub gc_hist_out: Option<PathBuf>,
    pub base_hist_out: Option<PathBuf>,
    pub entropy_hist_out: Option<PathBuf>,
    pub identity_hist_out: Option<PathBuf>,
    pub barcode_stats_out: Option<PathBuf>,
    pub k: usize,
    pub min_quality: u8,
    pub quality_in_offset: u8,
    pub quality_out_offset: u8,
    pub change_quality: bool,
    pub min_called_quality: u8,
    pub max_called_quality: u8,
    pub fake_quality: u8,
    pub fasta_wrap: usize,
    pub u_to_t: bool,
    pub to_upper_case: bool,
    pub lower_case_to_n: bool,
    pub dot_dash_x_to_n: bool,
    pub iupac_to_n: bool,
    pub fix_junk_and_iupac: bool,
    pub junk_mode: JunkMode,
    pub min_prob: f64,
    pub max_reads: Option<u64>,
    pub table_reads: Option<u64>,
    pub min_length: usize,
    pub trim_left: bool,
    pub trim_right: bool,
    pub trim_quality: f64,
    pub trim_optimal: bool,
    pub trim_optimal_bias: Option<f64>,
    pub trim_window: bool,
    pub trim_window_length: usize,
    pub trim_min_good_interval: usize,
    pub interleaved: bool,
    pub test_interleaved: bool,
    pub keep_all: bool,
    pub zero_bin: bool,
    pub deterministic: bool,
    pub rename_reads: bool,
    pub canonical: bool,
    pub remove_duplicate_kmers: bool,
    pub fix_spikes: bool,
    pub target_depth: u64,
    pub target_depth_first: Option<u64>,
    pub target_bad_percent_low: f64,
    pub target_bad_percent_high: f64,
    pub max_depth: Option<u64>,
    pub min_depth: u64,
    pub min_kmers_over_min_depth: usize,
    pub depth_percentile: f64,
    pub high_percentile: f64,
    pub low_percentile: f64,
    pub error_detect_ratio: u64,
    pub high_thresh: u64,
    pub low_thresh: u64,
    pub toss_error_reads: bool,
    pub toss_error_reads_first: bool,
    pub require_both_bad: bool,
    pub save_rare_reads: bool,
    pub discard_bad_only: bool,
    pub discard_bad_only_first: bool,
    pub error_correct: bool,
    pub error_correct_first: bool,
    pub error_correct_final: bool,
    pub overlap_error_correct: bool,
    pub overlap_error_correct_auto: bool,
    pub mark_errors_only: bool,
    pub mark_uncorrectable_errors: bool,
    pub trim_after_marking: bool,
    pub mark_with_one: bool,
    pub error_correct_ratio: u64,
    pub error_correct_high_thresh: u64,
    pub error_correct_low_thresh: u64,
    pub max_errors_to_correct: usize,
    pub max_quality_to_correct: u8,
    pub correct_from_left: bool,
    pub correct_from_right: bool,
    pub suffix_len: usize,
    pub prefix_len: usize,
    pub count_up: bool,
    pub add_bad_reads_countup: bool,
    pub use_lower_depth: bool,
    pub toss_by_low_true_depth: bool,
    pub low_bin_depth: i64,
    pub high_bin_depth: i64,
    pub hist_len: usize,
    pub side_hist_len: Option<usize>,
    pub gc_bins: Option<usize>,
    pub entropy_bins: usize,
    pub entropy_k: usize,
    pub entropy_window: usize,
    pub allow_entropy_ns: bool,
    pub identity_bins: usize,
    pub cardinality: CardinalitySettings,
    pub hist_columns: u8,
    pub print_zero_coverage: bool,
    pub peak_min_height: u64,
    pub peak_min_volume: u64,
    pub peak_min_width: usize,
    pub peak_min_peak: usize,
    pub peak_max_peak: usize,
    pub peak_max_count: usize,
    pub peak_ploidy: i32,
    pub overwrite: bool,
    pub append: bool,
    pub passes: usize,
    pub threads: Option<usize>,
    pub gzip_threads: Option<usize>,
    pub temp_dir: Option<PathBuf>,
    pub use_temp_dir: bool,
    pub max_countup_spill_initial_runs: Option<usize>,
    pub max_countup_spill_merge_runs: Option<usize>,
    pub max_countup_spill_final_runs: Option<usize>,
    pub max_countup_spill_live_bytes: Option<u64>,
    pub max_countup_spill_final_live_bytes: Option<u64>,
    pub max_countup_spill_write_bytes: Option<u64>,
    pub table_initial_size: Option<usize>,
    pub table_prealloc_fraction: Option<f64>,
    pub build_passes: usize,
    pub auto_count_min: bool,
    pub force_exact_counts: bool,
    pub auto_count_min_input_bytes: usize,
    pub auto_count_min_read_threshold: u64,
    pub auto_count_min_memory_bytes: Option<usize>,
    pub count_min: CountMinSettings,
    pub count_min_bits_first: Option<u8>,
    pub prefilter: PrefilterSettings,
    pub locked_increment: Option<bool>,
    pub gpu_counting: bool,
    pub gpu_helper: Option<PathBuf>,
    pub gpu_persistent: bool,
    pub notes: Vec<String>,

}

Fields§

§in1: Option<PathBuf>§in2: Option<PathBuf>§extra: Vec<PathBuf>§out1: Option<PathBuf>§out2: Option<PathBuf>§out_toss1: Option<PathBuf>§out_toss2: Option<PathBuf>§out_low1: Option<PathBuf>§out_low2: Option<PathBuf>§out_mid1: Option<PathBuf>§out_mid2: Option<PathBuf>§out_high1: Option<PathBuf>§out_high2: Option<PathBuf>§out_uncorrected1: Option<PathBuf>§out_uncorrected2: Option<PathBuf>§hist_in: Option<PathBuf>§hist_out: Option<PathBuf>§rhist_in: Option<PathBuf>§rhist_out: Option<PathBuf>§peaks_in: Option<PathBuf>§peaks_out: Option<PathBuf>§match_hist_out: Option<PathBuf>§insert_hist_out: Option<PathBuf>§quality_accuracy_hist_out: Option<PathBuf>§indel_hist_out: Option<PathBuf>§error_hist_out: Option<PathBuf>§quality_hist_out: Option<PathBuf>§base_quality_hist_out: Option<PathBuf>§quality_count_hist_out: Option<PathBuf>§average_quality_hist_out: Option<PathBuf>§overall_base_quality_hist_out: Option<PathBuf>§length_hist_out: Option<PathBuf>§gc_hist_out: Option<PathBuf>§base_hist_out: Option<PathBuf>§entropy_hist_out: Option<PathBuf>§identity_hist_out: Option<PathBuf>§barcode_stats_out: Option<PathBuf>§k: usize§min_quality: u8§quality_in_offset: u8§quality_out_offset: u8§change_quality: bool§min_called_quality: u8§max_called_quality: u8§fake_quality: u8§fasta_wrap: usize§u_to_t: bool§to_upper_case: bool§lower_case_to_n: bool§dot_dash_x_to_n: bool§iupac_to_n: bool§fix_junk_and_iupac: bool§junk_mode: JunkMode§min_prob: f64§max_reads: Option<u64>§table_reads: Option<u64>§min_length: usize§trim_left: bool§trim_right: bool§trim_quality: f64§trim_optimal: bool§trim_optimal_bias: Option<f64>§trim_window: bool§trim_window_length: usize§trim_min_good_interval: usize§interleaved: bool§test_interleaved: bool§keep_all: bool§zero_bin: bool§deterministic: bool§rename_reads: bool§canonical: bool§remove_duplicate_kmers: bool§fix_spikes: bool§target_depth: u64§target_depth_first: Option<u64>§target_bad_percent_low: f64§target_bad_percent_high: f64§max_depth: Option<u64>§min_depth: u64§min_kmers_over_min_depth: usize§depth_percentile: f64§high_percentile: f64§low_percentile: f64§error_detect_ratio: u64§high_thresh: u64§low_thresh: u64§toss_error_reads: bool§toss_error_reads_first: bool§require_both_bad: bool§save_rare_reads: bool§discard_bad_only: bool§discard_bad_only_first: bool§error_correct: bool§error_correct_first: bool§error_correct_final: bool§overlap_error_correct: bool§overlap_error_correct_auto: bool§mark_errors_only: bool§mark_uncorrectable_errors: bool§trim_after_marking: bool§mark_with_one: bool§error_correct_ratio: u64§error_correct_high_thresh: u64§error_correct_low_thresh: u64§max_errors_to_correct: usize§max_quality_to_correct: u8§correct_from_left: bool§correct_from_right: bool§suffix_len: usize§prefix_len: usize§count_up: bool§add_bad_reads_countup: bool§use_lower_depth: bool§toss_by_low_true_depth: bool§low_bin_depth: i64§high_bin_depth: i64§hist_len: usize§side_hist_len: Option<usize>§gc_bins: Option<usize>§entropy_bins: usize§entropy_k: usize§entropy_window: usize§allow_entropy_ns: bool§identity_bins: usize§cardinality: CardinalitySettings§hist_columns: u8§print_zero_coverage: bool§peak_min_height: u64§peak_min_volume: u64§peak_min_width: usize§peak_min_peak: usize§peak_max_peak: usize§peak_max_count: usize§peak_ploidy: i32§overwrite: bool§append: bool§passes: usize§threads: Option<usize>§gzip_threads: Option<usize>§temp_dir: Option<PathBuf>§use_temp_dir: bool§max_countup_spill_initial_runs: Option<usize>§max_countup_spill_merge_runs: Option<usize>§max_countup_spill_final_runs: Option<usize>§max_countup_spill_live_bytes: Option<u64>§max_countup_spill_final_live_bytes: Option<u64>§max_countup_spill_write_bytes: Option<u64>§table_initial_size: Option<usize>§table_prealloc_fraction: Option<f64>§build_passes: usize§auto_count_min: bool§force_exact_counts: bool§auto_count_min_input_bytes: usize§auto_count_min_read_threshold: u64§auto_count_min_memory_bytes: Option<usize>§count_min: CountMinSettings§count_min_bits_first: Option<u8>§prefilter: PrefilterSettings§locked_increment: Option<bool>§gpu_counting: bool§gpu_helper: Option<PathBuf>§gpu_persistent: bool§notes: Vec<String>

Trait Implementations§

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impl Clone for Config

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fn clone(&self) -> Config

Returns a duplicate of the value. Read more
1.0.0 (const: unstable) · Source§

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

Performs copy-assignment from source. Read more
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impl Debug for Config

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

Formats the value using the given formatter. Read more
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impl Default for Config

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fn default() -> Self

Returns the “default value” for a type. Read more

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impl<T> Any for T
where T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more
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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more
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impl<T> BorrowMut<T> for T
where T: ?Sized,

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fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more
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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)
Performs copy-assignment from self to dest. Read more
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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into<U> for T
where U: From<T>,

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fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> IntoEither for T

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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 more
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fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

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 more
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impl<T> Pointable for T

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const ALIGN: usize

The alignment of pointer.
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type Init = T

The type for initializers.
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unsafe fn init(init: <T as Pointable>::Init) -> usize

Initializes a with the given initializer. Read more
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unsafe fn deref<'a>(ptr: usize) -> &'a T

Dereferences the given pointer. Read more
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unsafe fn deref_mut<'a>(ptr: usize) -> &'a mut T

Mutably dereferences the given pointer. Read more
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unsafe fn drop(ptr: usize)

Drops the object pointed to by the given pointer. Read more
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impl<T> ToOwned for T
where T: Clone,

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type Owned = T

The resulting type after obtaining ownership.
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fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more
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fn clone_into(&self, target: &mut T)

Uses borrowed data to replace owned data, usually by cloning. Read more
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impl<T, U> TryFrom<U> for T
where U: Into<T>,

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type Error = Infallible

The type returned in the event of a conversion error.
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fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.
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type Error = <U as TryFrom<T>>::Error

The type returned in the event of a conversion error.
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fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.