Struct AugRefOpts 

pub struct AugRefOpts {

    pub genome: PathBuf,
    pub genes: PathBuf,
    pub out_dir: PathBuf,
    pub aug_type: Option<Vec<AugType>>,
    pub no_transcript: bool,
    pub read_length: i64,
    pub flank_trim_length: i64,
    pub no_flanking_merge: bool,
    pub filename_prefix: String,
    pub dedup_seqs: bool,
    pub extra_spliced: Option<PathBuf>,
    pub extra_unspliced: Option<PathBuf>,
    pub gff3: bool,
}

Fields

genome: PathBuf

The path to a genome fasta file.

genes: PathBuf

The path to a gene annotation gtf/gff3 file.

out_dir: PathBuf

The path to the output directory (will be created if it doesn’t exist).

aug_type: Option<Vec<AugType>>

Comma separated types of augmented sequences to include in the output FASTA file on top of spliced transcripts. Available options are intronic (or i for short), gene-body (or g), and transcript-body (or t).

no_transcript: bool

A flag of not including spliced transcripts in the output FASTA file. (usually there should be a good reason to do so)

read_length: i64

The read length of the single-cell experiment being processed (determines flank size).

flank_trim_length: i64

Determines the length of sequence subtracted from the read length to obtain the flank length.

no_flanking_merge: bool

Indicates whether flank lengths will be considered when merging introns.

filename_prefix: String

The file name prefix of the generated output files.

dedup_seqs: bool

Indicates whether identical sequences will be deduplicated.

extra_spliced: Option<PathBuf>

The path to an extra spliced sequence fasta file.

extra_unspliced: Option<PathBuf>

The path to an extra unspliced sequence fasta file.

gff3: bool

Denotes that the input annotation is a GFF3 (instead of GTF) file

Trait Implementations

impl Args for AugRefOpts

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

fn augment_args<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_args_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

impl Clone for AugRefOpts

fn clone(&self) -> AugRefOpts

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AugRefOpts

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

Formats the value using the given formatter.

impl FromArgMatches for AugRefOpts

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Serialize for AugRefOpts

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.