Struct AlignQuantOptions 

pub struct AlignQuantOptions {

    pub bam: PathBuf,
    pub output_dir: PathBuf,
    pub lib_type: String,
    pub em: EmOptions,
    pub range_factorization_bins: u32,
    pub score_exp: f64,
    pub transcripts: Option<PathBuf>,
    pub no_error_model: bool,
    pub seq_bias: bool,
    pub gc_bias: bool,
    pub pos_bias: bool,
    pub incompat_prior: f64,
    pub fld_mean: f64,
    pub fld_sd: f64,
    pub fld_max: usize,
    pub forgetting_factor: f64,
    pub init_uniform: bool,
    pub sig_digits: u32,
    pub num_error_bins: usize,
    pub discard_orphans: bool,
    pub bias_speed_samp: usize,
    pub num_aux_model_samples: u64,
    pub no_bias_length_threshold: bool,
    pub gc_bins: usize,
    pub cond_gc_bins: usize,
    pub skip_quant: bool,
    pub num_pre_aux_model_samples: u64,
    pub progress: Option<Arc<ProgressCounters>>,
}

Options for alignment-based quantification.

Fields

bam: PathBuf

BAM of alignments to the transcriptome (records grouped by read name)

output_dir: PathBuf

output directory

lib_type: String

library type string (recorded in output)

em: EmOptions

EM/VBEM options

range_factorization_bins: u32

range-factorization bins (0 disables)

score_exp: f64

soft-weight decay applied to alignment-score differences

transcripts: Option<PathBuf>

transcriptome FASTA (-t); required to train the alignment error model

no_error_model: bool

disable the alignment error model (salmon’s --noErrorModel)

seq_bias: bool

enable sequence-specific bias correction (--seqBias)

gc_bias: bool

enable fragment-GC bias correction (--gcBias)

pos_bias: bool

enable positional bias correction (--posBias)

incompat_prior: f64

weight multiplier for orientation-incompatible alignments; 0 drops them (salmon’s default ignoreIncompat behavior)

fld_mean: f64

fragment-length distribution prior mean, SD, and max tracked length (--fldMean / --fldSD / --fldMax)

fld_sd: f64

fld_max: usize

forgetting_factor: f64

online-phase forgetting factor (--forgettingFactor, salmon default 0.65)

init_uniform: bool

initialize the EM uniformly instead of with the online-estimate-blended warm start (--initUniform)

sig_digits: u32

significant digits for the EffectiveLength and NumReads columns of quant.sf (--sigDigits, salmon default 3)

num_error_bins: usize

number of read-position bins in the alignment error model (--numErrorBins, salmon default 4)

discard_orphans: bool

drop orphan (single-mate) placements in a paired library instead of fragment-length-penalizing them (--discardOrphans, alignment mode)

bias_speed_samp: usize

fragment-length sampling stride for the GC bias convolution (--biasSpeedSamp, default 5)

num_aux_model_samples: u64

online-phase auxiliary-model training window (--numAuxModelSamples, default 5,000,000)

no_bias_length_threshold: bool

disable the lower barrier on bias-corrected effective lengths (--noBiasLengthThreshold)

gc_bins: usize

GC bias model bin counts (--numGCBins × --conditionalGCBins, 25×3)

cond_gc_bins: usize

skip_quant: bool

skip abundance estimation + quant.sf, emitting only eq-classes, library type, and metadata (salmon’s --skipQuant)

num_pre_aux_model_samples: u64

fragments processed before the FLD aux model is applied (salmon’s --numPreAuxModelSamples; prior hardcoded value 5,000)

progress: Option<Arc<ProgressCounters>>

Optional shared progress counters. When Some, the BAM pass reports processed/mapped fragment counts here as it runs so the caller can drive a live progress display. None (the default) disables sharing.

Implementations

impl AlignQuantOptions

pub fn new(bam: PathBuf, output_dir: PathBuf) -> Self

Trait Implementations

impl Clone for AlignQuantOptions

fn clone(&self) -> AlignQuantOptions

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AlignQuantOptions

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

Formats the value using the given formatter.