Struct RawSequenceRead

pub struct RawSequenceRead {
    pub sequence: String,
    /* private fields */
}

A struct to hold the raw sequencing information and transform it if there are sequencing errors

Fields

sequence: String

Implementations

impl RawSequenceRead

pub fn new() -> Self

pub fn new_fill( line_1: String, line_2: String, line_3: String, line_4: String, ) -> RawSequenceRead

pub fn add_line(&mut self, line_num: u16, line: String) -> Result<()>

pub fn pack(&self) -> String

pub fn unpack(raw_string: String) -> Result<Self>

pub fn insert_barcodes_constant_region( &mut self, format_string: &str, best_sequence: String, )

Replaces the ’N’s in the sequencing format with the barcodes to fix any sequencing errrors that would cause the regex search not to work

pub fn fix_constant_region( &mut self, format_string: &str, max_constant_errors: u16, )

Fixes the constant region by finding the closest match within the full seqeuence that has fewer than the max errors allowed, then uses the format string to flip the barcodes into the ’N’s and have a fixed constant region string

pub fn quality_scores(&self) -> Vec<u8>

Each DNA base read score within FASTQ is the ascii number - 33. This returns the number scores associated with the ascii values

Score Error Probability 40 0.0001 30 0.001 20 0.01 10 0.1

pub fn low_quality( &self, min_average: f32, barcode_indicator_string: &str, start: usize, ) -> bool

Test for if any of the barcode average quality score falls below the min_average cutoff

pub fn check_fastq_format(&self) -> Result<()>

Trait Implementations

impl Clone for RawSequenceRead

fn clone(&self) -> RawSequenceRead

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Default for RawSequenceRead

fn default() -> Self

Returns the “default value” for a type.

impl Display for RawSequenceRead

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

Formats the value using the given formatter.