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::*;
use fastqrab_dna::dna::HitRegion;

/// Cut a fixed number of bases from the start of reads
#[derive(Clone, JsonSchema)]
#[tpd]
#[derive(Debug)]
pub struct CutStart {
    n: usize,
    #[schemars(with = "String")]
    #[tpd(adapt_in_verify(String))]
    segment: SegmentIndex,
    #[tpd(default)]
    #[tpd(alias = "if_label")]
    if_tag: Option<ConditionalTagLabel>,
}

impl VerifyIn<PartialConfig> for PartialCutStart {
    fn verify(
        &mut self,
        parent: &PartialConfig,
        _options: &VerifyOptions,
    ) -> std::result::Result<(), ValidationFailure>
    where
        Self: Sized + toml_pretty_deser::Visitor,
    {
        self.segment.validate_segment(parent);
        // self.n.verify(|v| { cutting 0 is fine, if no-opy.
        //     if *v == 0 {
        //         Err(ValidationFailure::new(
        //             "n must be > 0",
        //             Some("Set to a positive integer."),
        //         ))
        //     } else {
        //         Ok(())
        //     }
        // });
        Ok(())
    }
}

impl TagUser for PartialTaggedVariant<PartialCutStart> {
    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 {
                used_tags: vec![inner.if_tag.to_used_tag(&[])],
                must_see_all_tags: true,
                ..Default::default()
            })
        } else {
            None // cov:excl-line
        }
    }
}

impl Step for CutStart {
    fn apply(
        &self,
        mut block: FastQBlocksCombined,
        _input_info: &InputInfo,
        _demultiplex_info: &OptDemultiplex,
    ) -> anyhow::Result<(FastQBlocksCombined, bool)> {
        let condition = self
            .if_tag
            .as_ref()
            .map(|tag| get_bool_vec_from_tag(&block, tag));

        block.apply_in_place(
            self.segment,
            |read| read.cut_start(self.n),
            condition.as_deref(),
        );

        block.filter_tag_locations(
            self.segment,
            |location: HitRegion, _pos, _seq, _read_len: usize| -> NewLocation {
                if location.start < self.n {
                    NewLocation::Remove
                } else {
                    NewLocation::New(HitRegion {
                        start: location.start - self.n,
                        len: location.len,
                        segment_index: location.segment_index,
                    })
                }
            },
            condition.as_deref(),
        );

        Ok((block, true))
    }
}