Struct AlignOptions 

pub struct AlignOptions {

    pub index: String,
    pub reads_unpaired: Vec<String>,
    pub reads_1: Vec<String>,
    pub reads_2: Vec<String>,
    pub sam_file: Option<String>,
    pub fastq: bool,
    pub fasta: bool,
    pub sequences: bool,
    pub skip: Option<usize>,
    pub upto: Option<usize>,
    pub trim5: Option<usize>,
    pub trim3: Option<usize>,
    pub seed_mismatches: Option<u8>,
    pub seed_length: usize,
    pub end_to_end: bool,
    pub local: bool,
    pub no_forward: bool,
    pub no_reverse: bool,
    pub match_bonus: Option<i32>,
    pub mismatch_penalty: i32,
    pub n_penalty: i32,
    pub read_gap: Option<String>,
    pub ref_gap: Option<String>,
    pub report_alignments: Option<usize>,
    pub report_all: bool,
    pub failed_extends: usize,
    pub seed_sets: usize,
    pub min_insert: usize,
    pub max_insert: usize,
    pub orientation: Option<String>,
    pub threads: usize,
    pub reorder: bool,
    pub print_time: bool,
    pub quiet: bool,
    pub no_unaligned: bool,
    pub no_head: bool,
    pub no_sq: bool,
    pub xeq: bool,
}

Ferroux aligner - Fast and sensitive read alignment

Ferroux is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Fields

index: String

Index filename prefix (minus trailing .X.rai)

reads_unpaired: Vec<String>

Files with unpaired reads

reads_1: Vec<String>

Files with #1 mates, paired with files in

reads_2: Vec<String>

Files with #2 mates, paired with files in

sam_file: Option<String>

Output SAM file (default: stdout)

fastq: bool

Query input files are FASTQ .fq/.fastq (default)

fasta: bool

Query input files are (multi-)FASTA .fa/.mfa

sequences: bool

, , are sequences themselves, not files

skip: Option<usize>

Skip the first reads/pairs in the input

upto: Option<usize>

Stop after first reads/pairs

trim5: Option<usize>

Trim bases from 5’/left end of reads

trim3: Option<usize>

Trim bases from 3’/right end of reads

seed_mismatches: Option<u8>

Max # mismatches in seed alignment; can be 0 or 1

seed_length: usize

Length of seed substrings; must be >3, <32

end_to_end: bool

Entire read must align; no clipping

local: bool

Local alignment; ends might be soft clipped

no_forward: bool

Do not align forward (original) version of read

no_reverse: bool

Do not align reverse-complement version of read

match_bonus: Option<i32>

Match bonus (0 for –end-to-end, 2 for –local)

mismatch_penalty: i32

Max penalty for mismatch

n_penalty: i32

Penalty for non-A/C/G/Ts in read/ref

read_gap: Option<String>

Read gap open, extend penalties

ref_gap: Option<String>

Reference gap open, extend penalties

report_alignments: Option<usize>

Report up to alignments per read

report_all: bool

Report all alignments

failed_extends: usize

Give up extending after failed extends

seed_sets: usize

For reads with repetitive seeds, try sets of seeds

min_insert: usize

Minimum fragment length

max_insert: usize

Maximum fragment length

orientation: Option<String>

-1, -2 mates align fw/rev, rev/fw, fw/fw

threads: usize

Number of alignment threads

reorder: bool

Force SAM output order to match input

print_time: bool

Print wall-clock time taken by search phases

quiet: bool

Print nothing to stderr except serious errors

no_unaligned: bool

Suppress SAM records for unaligned reads

no_head: bool

Suppress header lines (@PG, @HD, etc.)

no_sq: bool

Suppress @SQ header lines

xeq: bool

Use ‘=’/‘X’, instead of ‘M,’ to specify matches/mismatches

Trait Implementations

impl Args for AlignOptions

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 CommandFactory for AlignOptions

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for AlignOptions

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

Formats the value using the given formatter.

impl FromArgMatches for AlignOptions

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 Parser for AlignOptions

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.