fastqrab-steps 0.9.1

Pipeline building blocks for fastqrab: read transformations, filters, reports, and demultiplexing
Documentation 
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use crate::transformations::prelude::*;

/// Count the number of N. See `CalcBaseContent` for general case
#[derive(Clone, JsonSchema)]
#[tpd]
#[derive(Debug)]
pub struct NContent {
    pub out_label: TagLabel,
    #[schemars(with = "String")]
    #[tpd(adapt_in_verify(String))]
    pub segment: SegmentIndexOrAll,

    #[tpd(alias = "rate")]
    pub relative: bool,
}

impl VerifyIn<PartialConfig> for PartialNContent {
    fn verify(
        &mut self,
        parent: &PartialConfig,
        _options: &VerifyOptions,
    ) -> std::result::Result<(), ValidationFailure>
    where
        Self: Sized + toml_pretty_deser::Visitor,
    {
        self.segment.validate_segment(parent);
        Ok(())
    }
}

// cov:excl-start
impl TagUser for PartialTaggedVariant<PartialNContent> {
    #[mutants::skip]
    fn get_tag_usage(
        &mut self,
        _tags_available: &IndexMap<TagLabel, TagMetadata>,
        _segment_order: &[String],
    ) -> Option<TagUsageInfo<'_>> {
        //unreachable!("Should have been swapped for BaseCount in expansion");
        //this is totally rechable since we *must* call get_tag_usage on not-fully
        //validated transforms
        None
    }
}

impl Step for NContent {
    fn apply(
        &self,
        _block: FastQBlocksCombined,
        _input_info: &InputInfo,
        _demultiplex_info: &OptDemultiplex,
    ) -> anyhow::Result<(FastQBlocksCombined, bool)> {
        bail!("ExtractNContent is converted into ExtractBaseContent during expansion")
    }
}
// cov:excl-stop