fastqrab-steps 0.9.1

Pipeline building blocks for fastqrab: read transformations, filters, reports, and demultiplexing
Documentation 
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use typed_floats::tf64::NonNaN;

use super::extract_numeric_tags_plus_all;
use crate::transformations::prelude::*;

/// Calculate complexity score (# transitions / (len -1))
#[derive(Clone, JsonSchema)]
#[tpd]
#[derive(Debug)]
pub struct Complexity {
    pub out_label: TagLabel,

    #[schemars(with = "String")]
    #[tpd(adapt_in_verify(String))]
    segment: SegmentIndexOrAll,
}

impl VerifyIn<PartialConfig> for PartialComplexity {
    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(())
    }
}

impl TagUser for PartialTaggedVariant<PartialComplexity> {
    fn get_tag_usage(
        &mut self,
        _tags_available: &IndexMap<TagLabel, TagMetadata>,
        _segment_order: &[String],
    ) -> Option<TagUsageInfo<'_>> {
        if let Some(inner) = self.toml_value.value.as_mut() {
            Some(TagUsageInfo {
                declared_tag: inner.out_label.to_declared_tag(TagValueType::Numeric((
                    Some(NonNaN::new(0.0).expect("can't fail")),
                    Some(NonNaN::new(1.0).expect("can't fail")),
                ))),
                ..Default::default()
            })
        } else {
            None // cov:excl-line
        }
    }
}

impl Step for Complexity {
    fn apply(
        &self,
        mut block: FastQBlocksCombined,
        _input_info: &InputInfo,
        _demultiplex_info: &OptDemultiplex,
    ) -> anyhow::Result<(FastQBlocksCombined, bool)> {
        #[expect(
            clippy::cast_precision_loss,
            reason = "Read lengths unlikely to exceed f64 precise regions"
        )]
        extract_numeric_tags_plus_all(
            self.segment,
            &self.out_label,
            |read| {
                // Calculate the number of transitions
                let mut transitions = 0;
                let seq = read.seq();
                if seq.len() <= 1 {
                    return 0.0;
                }
                for ii in 0..seq.len() - 1 {
                    if seq[ii] != seq[ii + 1] {
                        transitions += 1;
                    }
                }
                f64::from(transitions) / (seq.len() - 1) as f64
            },
            |reads| {
                let mut total_transitions = 0usize;
                let mut total_positions = 0usize;

                // Process all reads
                for read in reads {
                    let seq = read.seq();
                    if seq.len() > 1 {
                        for ii in 0..seq.len() - 1 {
                            if seq[ii] != seq[ii + 1] {
                                total_transitions += 1;
                            }
                        }
                        total_positions += seq.len() - 1;
                    }
                }
                if total_positions == 0 {
                    0.0
                } else {
                    total_transitions as f64 / total_positions as f64
                }
            },
            &mut block,
        );

        Ok((block, true))
    }
}