ferro-hgvs 0.6.0

//! `VariantProjector` orchestrator.

use crate::data::mapping::MappingInfo;
use crate::data::projection::Projector;
use crate::error::FerroError;
use crate::hgvs::edit::NaEdit;
use crate::hgvs::interval::{CdsInterval, TxInterval};
use crate::hgvs::location::{CdsPos, GenomePos, TxPos};
use crate::hgvs::variant::{
    is_frameshift, AlleleVariant, CdsVariant, HgvsVariant, LocEdit, TxVariant,
};
use crate::normalize::{NormalizeConfig, Normalizer};
use crate::project::accession::parse_accession;
use crate::project::edit::transform_edit_for_strand;
use crate::project::protein::{predict_indel_protein, predict_substitution_protein};
use crate::project::result::VariantProjection;
use crate::reference::ReferenceProvider;

pub struct VariantProjector<P: ReferenceProvider + Clone> {
    projector: Projector,
    provider: P,
    normalizer: Normalizer<P>,
}

impl<P: ReferenceProvider + Clone> VariantProjector<P> {
    pub fn new(projector: Projector, provider: P) -> Self {
        let normalizer = Normalizer::with_config(provider.clone(), NormalizeConfig::default());
        Self {
            projector,
            provider,
            normalizer,
        }
    }

    pub fn with_normalize_config(mut self, config: NormalizeConfig) -> Self {
        self.normalizer = Normalizer::with_config(self.provider.clone(), config);
        self
    }

    /// Parse, normalize, and project an HGVS string onto a transcript.
    pub fn project(
        &self,
        hgvs_string: &str,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        let variant = crate::parse_hgvs(hgvs_string)?;
        self.project_variant(&variant, transcript_id)
    }

    /// Normalize and project an already-parsed g. variant onto a transcript.
    ///
    /// The variant is normalized first; for pre-normalized variants use
    /// [`project_normalized`] to skip the redundant normalization step.
    pub fn project_variant(
        &self,
        variant: &HgvsVariant,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        // 1. Normalize the genomic variant. The normalizer is built once at
        // construction time so we don't clone the (potentially heavy) provider
        // on every call.
        let normalized = self.normalizer.normalize(variant)?;
        self.project_variant_inner(&normalized, transcript_id)
    }

    /// Project an already-normalized g. variant onto a transcript, skipping the
    /// normalization step.
    ///
    /// Callers that pre-normalize once and then project against many transcripts
    /// should use this method to avoid the cost of re-normalization.
    ///
    /// **Warning**: passing a non-normalized variant will produce coordinates
    /// that are technically valid but may not match other tools' canonical form.
    pub fn project_normalized(
        &self,
        variant: &HgvsVariant,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        self.project_variant_inner(variant, transcript_id)
    }

    /// Parse, normalize, and project an HGVS string onto ALL overlapping
    /// transcripts, returning results in clinical priority order (MANE Select
    /// first, then Plus Clinical, then canonical, then longest CDS).
    ///
    /// Returns an empty `Vec` when the variant overlaps no known transcripts.
    /// Individual transcript errors are logged at trace level and silently
    /// skipped so that a single bad transcript does not abort the whole call.
    pub fn project_all(&self, hgvs_string: &str) -> Result<Vec<VariantProjection>, FerroError> {
        let variant = crate::parse_hgvs(hgvs_string)?;
        self.project_variant_all(&variant)
    }

    /// Normalize and project an already-parsed g. variant onto ALL overlapping
    /// transcripts.
    ///
    /// See [`project_all`] for ordering and error-handling semantics.
    pub fn project_variant_all(
        &self,
        variant: &HgvsVariant,
    ) -> Result<Vec<VariantProjection>, FerroError> {
        // 1. Normalize once via the cached normalizer (built at construction time).
        let normalized = self.normalizer.normalize(variant)?;
        self.project_normalized_all(&normalized)
    }

    /// Project an already-normalized g. variant onto ALL overlapping
    /// transcripts, skipping re-normalization.
    ///
    /// Callers that pre-normalize once and then fan-out across transcripts
    /// should use this method.
    pub fn project_normalized_all(
        &self,
        variant: &HgvsVariant,
    ) -> Result<Vec<VariantProjection>, FerroError> {
        // 2. Extract contig + first-base position from the normalized variant.
        //    For Allele variants we use the first inner variant's accession.
        let (contig, pos) = extract_contig_and_pos(variant)?;

        // 3. Find overlapping transcripts via the Projector (sorted by priority).
        let projection_result = self.projector.project(&contig, pos)?;

        // 4. Project against each overlapping transcript.
        let mut results = Vec::with_capacity(projection_result.projections.len());
        for tx_proj in &projection_result.projections {
            match self.project_variant_inner(variant, &tx_proj.transcript_id) {
                Ok(vp) => results.push(vp),
                Err(e) => {
                    // Skip transcripts that fail — log at trace level only.
                    log::trace!(
                        "project_normalized_all: skipping {} for {}: {}",
                        tx_proj.transcript_id,
                        variant,
                        e
                    );
                }
            }
        }

        Ok(results)
    }

    // -------------------------------------------------------------------------
    // Private helpers
    // -------------------------------------------------------------------------

    /// Core projection logic, operating on a variant that is assumed to be
    /// already normalized.  Does NOT re-normalize.
    fn project_variant_inner(
        &self,
        variant: &HgvsVariant,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        // Dispatch on variant kind.
        match variant {
            HgvsVariant::Allele(allele) => {
                self.project_allele_inner(allele, variant, transcript_id)
            }
            _ => self.project_single_inner(variant, transcript_id),
        }
    }

    /// Project a compound [`AlleleVariant`] by recursively projecting each
    /// inner variant and combining the results.
    fn project_allele_inner(
        &self,
        allele: &AlleleVariant,
        original: &HgvsVariant,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        // Empty allele: pass through with no coding/protein, but validate the
        // transcript ID — every other path through `project_variant_inner` errors
        // out for unknown transcripts (via `project_single_inner`), and this
        // branch must behave the same to avoid silently returning bogus
        // projections for typo'd or missing accessions.
        if allele.variants.is_empty() {
            let gene_symbol = self
                .projector
                .mapper()
                .cdot()
                .get_transcript(transcript_id)
                .ok_or_else(|| FerroError::ReferenceNotFound {
                    id: transcript_id.to_string(),
                })?
                .gene_name
                .clone();
            return Ok(VariantProjection {
                genomic: original.clone(),
                coding: None,
                protein: None,
                transcript_id: transcript_id.to_string(),
                gene_symbol,
                is_frameshift: false,
                is_intronic: false,
                is_utr: false,
            });
        }

        // Recursively project each inner variant.
        let mut inner_projections = Vec::with_capacity(allele.variants.len());
        for inner in &allele.variants {
            let proj = self.project_variant_inner(inner, transcript_id)?;
            inner_projections.push(proj);
        }

        // Aggregate flags.
        let is_frameshift = inner_projections.iter().any(|p| p.is_frameshift);
        let is_intronic = inner_projections.iter().any(|p| p.is_intronic);
        let is_utr = inner_projections.iter().any(|p| p.is_utr);

        // gene_symbol from any projection that has one.
        let gene_symbol = inner_projections.iter().find_map(|p| p.gene_symbol.clone());

        // Build the coding allele from inner c./n. variants.
        let coding_variants: Option<Vec<HgvsVariant>> =
            inner_projections.iter().map(|p| p.coding.clone()).collect();
        let coding = coding_variants
            .map(|variants| HgvsVariant::Allele(AlleleVariant::new(variants, allele.phase)));

        // Build the protein allele only if ALL inner projections have a protein.
        let all_have_protein = inner_projections.iter().all(|p| p.protein.is_some());
        let protein = if all_have_protein {
            let protein_variants: Vec<HgvsVariant> = inner_projections
                .iter()
                .filter_map(|p| p.protein.clone())
                .collect();
            Some(HgvsVariant::Allele(AlleleVariant::new(
                protein_variants,
                allele.phase,
            )))
        } else {
            None
        };

        Ok(VariantProjection {
            genomic: original.clone(),
            coding,
            protein,
            transcript_id: transcript_id.to_string(),
            gene_symbol,
            is_frameshift,
            is_intronic,
            is_utr,
        })
    }

    /// Project a single (non-allele) g. variant, assuming it has already been
    /// normalized.
    fn project_single_inner(
        &self,
        normalized: &HgvsVariant,
        transcript_id: &str,
    ) -> Result<VariantProjection, FerroError> {
        // Require a g. variant.
        let genome_variant = match normalized {
            HgvsVariant::Genome(g) => g.clone(),
            _ => {
                return Err(FerroError::UnsupportedProjection {
                    reason: "VariantProjector currently only accepts g. variants".to_string(),
                });
            }
        };

        let edit = genome_variant
            .loc_edit
            .edit
            .inner()
            .cloned()
            .ok_or_else(|| FerroError::UnsupportedProjection {
                reason: "g. variant has no concrete edit".to_string(),
            })?;

        // Look up the transcript in the cdot mapper.
        let cdot_tx = self
            .projector
            .mapper()
            .cdot()
            .get_transcript(transcript_id)
            .ok_or_else(|| FerroError::ReferenceNotFound {
                id: transcript_id.to_string(),
            })?;
        let strand = cdot_tx.strand;
        let gene_symbol = cdot_tx.gene_name.clone();
        let cdot_protein = cdot_tx.protein.clone();
        let is_coding = cdot_tx.cds_start.is_some();

        // Extract start and end genomic positions from the variant interval.
        let g_start = genome_variant
            .loc_edit
            .location
            .start
            .inner()
            .cloned()
            .ok_or_else(|| FerroError::InvalidCoordinates {
                msg: "genomic interval start is unknown".to_string(),
            })?;
        let g_end = genome_variant
            .loc_edit
            .location
            .end
            .inner()
            .cloned()
            .ok_or_else(|| FerroError::InvalidCoordinates {
                msg: "genomic interval end is unknown".to_string(),
            })?;

        let mapper = self.projector.mapper();
        let normalized_str = normalized.to_string();

        // Compute the overall genomic extent of the transcript from its exons.
        // Exon format: [genome_start(0-based), genome_end(0-based excl), tx_start, tx_end].
        let (tx_genome_start, tx_genome_end) = {
            let exons = &cdot_tx.exons;
            if exons.is_empty() {
                return Err(FerroError::ReferenceNotFound {
                    id: transcript_id.to_string(),
                });
            }
            let starts = exons.iter().map(|e| e[0]).min().unwrap();
            let ends = exons.iter().map(|e| e[1]).max().unwrap();
            (starts, ends)
        };

        // Helper: map one GenomePos → CdsPos, converting out-of-range errors.
        let map_position = |gp: &GenomePos| -> Result<(CdsPos, MappingInfo), FerroError> {
            if gp.base < tx_genome_start || gp.base >= tx_genome_end {
                return Err(FerroError::TranscriptNotOverlapping {
                    variant: normalized_str.clone(),
                    transcript_id: transcript_id.to_string(),
                });
            }
            match mapper.genome_to_cds(transcript_id, gp) {
                Ok(res) => Ok((res.variant, res.info)),
                Err(FerroError::InvalidCoordinates { .. })
                | Err(FerroError::ConversionError { .. }) => {
                    Err(FerroError::TranscriptNotOverlapping {
                        variant: normalized_str.clone(),
                        transcript_id: transcript_id.to_string(),
                    })
                }
                Err(other) => Err(other),
            }
        };

        let (cds_start_raw, info_start) = map_position(&g_start)?;
        let (cds_end_raw, info_end) = map_position(&g_end)?;

        // On minus strand the start and end of the c. interval are swapped.
        let (cds_start, cds_end) = match strand {
            crate::reference::Strand::Plus => (cds_start_raw, cds_end_raw),
            crate::reference::Strand::Minus => (cds_end_raw, cds_start_raw),
            crate::reference::Strand::Unknown => {
                return Err(FerroError::UnsupportedProjection {
                    reason: format!(
                        "transcript {} has unknown strand; cannot project g. → c./n.",
                        transcript_id
                    ),
                });
            }
        };

        // Transform the edit for the transcript strand.
        let c_edit = transform_edit_for_strand(&edit, strand);

        // Build the c./n. HGVS variant.
        let coding = if is_coding {
            let interval = CdsInterval::new(cds_start, cds_end);
            HgvsVariant::Cds(CdsVariant {
                accession: parse_accession(transcript_id),
                gene_symbol: gene_symbol.clone(),
                loc_edit: LocEdit::new(interval, c_edit.clone()),
            })
        } else {
            let tx_start = TxPos::new(cds_start.base);
            let tx_end = TxPos::new(cds_end.base);
            HgvsVariant::Tx(TxVariant {
                accession: parse_accession(transcript_id),
                gene_symbol: gene_symbol.clone(),
                loc_edit: LocEdit::new(TxInterval::new(tx_start, tx_end), c_edit.clone()),
            })
        };

        // Derive per-position flags from MappingInfo.
        let is_intronic = info_start.is_intronic || info_end.is_intronic;
        let is_utr = !is_intronic
            && (info_start.in_5utr || info_start.in_3utr || info_end.in_5utr || info_end.in_3utr);

        // Predict protein consequence for CDS variants.
        let mut protein = None;
        if !is_intronic && !is_utr && is_coding {
            // Prefer the explicit cdot.protein accession; otherwise infer NP_/XP_
            // from NM_/XM_ by stripping the prefix (not by substring replace, which
            // would mangle accessions whose suffix happens to contain "NM_"). If
            // we cannot infer a protein accession, skip protein prediction rather
            // than fabricate a bogus one.
            let prot_acc = match cdot_protein {
                Some(p) => Some(p),
                None => transcript_id
                    .strip_prefix("NM_")
                    .map(|rest| format!("NP_{rest}"))
                    .or_else(|| {
                        transcript_id
                            .strip_prefix("XM_")
                            .map(|rest| format!("XP_{rest}"))
                    }),
            };
            if let Some(prot_acc) = prot_acc {
                match &c_edit {
                    NaEdit::Substitution { .. } => {
                        let tx_for_codon = self.provider.get_transcript(transcript_id)?;
                        protein = Some(predict_substitution_protein(
                            &tx_for_codon,
                            cds_start.base,
                            &c_edit,
                            &prot_acc,
                        )?);
                    }
                    NaEdit::Deletion { .. }
                    | NaEdit::Insertion { .. }
                    | NaEdit::Duplication { .. }
                    | NaEdit::Delins { .. }
                    | NaEdit::Inversion { .. }
                        // Only predict when both CDS positions are concrete exonic positions
                        // (no intronic offsets — already guarded above).
                        if cds_start.offset.is_none()
                            && cds_end.offset.is_none()
                            && cds_start.base > 0
                            && cds_end.base > 0 =>
                    {
                        let tx_for_codon = self.provider.get_transcript(transcript_id)?;
                        match predict_indel_protein(
                            &tx_for_codon,
                            cds_start.base,
                            cds_end.base,
                            &c_edit,
                            &prot_acc,
                        ) {
                            Ok(pv) => protein = Some(pv),
                            // Non-fatal: unsupported edits or missing sequence → leave protein=None.
                            Err(FerroError::UnsupportedProjection { .. })
                            | Err(FerroError::ProteinSequenceUnavailable { .. }) => {}
                            Err(other) => return Err(other),
                        }
                    }
                    _ => {}
                }
            }
        }

        let frameshift = is_frameshift(&coding);
        Ok(VariantProjection {
            genomic: normalized.clone(),
            coding: Some(coding),
            protein,
            transcript_id: transcript_id.to_string(),
            gene_symbol,
            is_frameshift: frameshift,
            is_intronic,
            is_utr,
        })
    }
}

/// Extract the contig name and a representative 1-based genomic position from
/// an already-normalized `HgvsVariant`.
///
/// For `HgvsVariant::Allele`, the first inner g. variant is used.
///
/// # Contig name resolution
///
/// The contig name is taken directly from the variant's `Accession`. For
/// standard RefSeq genomic accessions (e.g. `NC_000001.11`) the cdot mapper
/// stores contigs under those same names and also aliases UCSC names
/// (`chr1`) to them via `populate_contig_aliases`.  For assembly-notation
/// accessions (`GRCh38(chr1)`) the `chromosome` field of `Accession` is
/// used instead.  Callers that use non-standard accession formats (e.g.
/// plain `chr1` keys) should ensure their cdot data was loaded with matching
/// contig keys.
fn extract_contig_and_pos(variant: &HgvsVariant) -> Result<(String, u64), FerroError> {
    let effective = match variant {
        HgvsVariant::Allele(allele) => {
            allele
                .variants
                .first()
                .ok_or_else(|| FerroError::UnsupportedProjection {
                    reason: "cannot project an empty allele to all transcripts".to_string(),
                })?
        }
        other => other,
    };

    match effective {
        HgvsVariant::Genome(gv) => {
            // Prefer the chromosome field for assembly-notation accessions.
            let contig = if let Some(chr) = &gv.accession.chromosome {
                chr.to_string()
            } else {
                gv.accession.full()
            };

            let pos = gv
                .loc_edit
                .location
                .start
                .inner()
                .cloned()
                .ok_or_else(|| FerroError::InvalidCoordinates {
                    msg: "genomic interval start is unknown".to_string(),
                })?
                .base;

            Ok((contig, pos))
        }
        _ => Err(FerroError::UnsupportedProjection {
            reason: "project_all currently only accepts g. variants".to_string(),
        }),
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::data::cdot::{CdotMapper, CdotTranscript};
    use crate::data::projection::Projector;
    use crate::hgvs::variant::{AllelePhase, AlleleVariant};
    use crate::reference::mock::MockProvider;
    use crate::reference::transcript::{Exon, ManeStatus, Strand as TxStrand, Transcript};
    use crate::reference::Strand as ProvStrand;
    use std::sync::OnceLock;

    fn make_test_provider_and_projector() -> (Projector, MockProvider) {
        // A single coding transcript on chr1, plus strand.
        //
        // Genomic layout (cdot 0-based coords):
        //   Exon: genome [1000, 1009), tx [0, 9), so 9 bases total.
        //   cds_start = 0 (0-based, no 5'UTR), cds_end = 9.
        //
        // Sequence: "ATGCGCTAA" = Met-Arg-Stop (3 codons).
        //
        // Coordinate mapping (cdot genome 0-based → HGVS c. 1-based):
        //   g.1000 → tx_pos=0 → c.1 (A = first base of Met)
        //   g.1001 → tx_pos=1 → c.2 (T)
        //   g.1002 → tx_pos=2 → c.3 (G)
        //   g.1003 → tx_pos=3 → c.4 (C ← ref base for test substitution)
        //   g.1004 → tx_pos=4 → c.5 (G)
        //   ...
        //
        // c.4C>A: codon 2 CGC (Arg) → AGC (Ser), missense.
        let mut cdot = CdotMapper::new();
        cdot.add_transcript(
            "NM_TEST.1".to_string(),
            CdotTranscript {
                gene_name: Some("TESTGENE".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Plus,
                // [genome_start(0-based), genome_end(0-based excl), tx_start(1-based), tx_end(1-based)]
                exons: vec![[1000, 1009, 0, 9]],
                cds_start: Some(0), // 0-based: CDS starts at tx_pos 0 (no 5'UTR)
                cds_end: Some(9),   // 0-based exclusive: CDS ends at tx_pos 9
                gene_id: None,
                protein: Some("NP_TEST.1".to_string()),
                exon_cigars: Vec::new(),
            },
        );
        let projector = Projector::new(cdot);

        let mut provider = MockProvider::new();
        // Transcript: sequence "ATGCGCTAA", cds_start=1 (1-based, first base).
        provider.add_transcript(Transcript {
            id: "NM_TEST.1".to_string(),
            gene_symbol: Some("TESTGENE".to_string()),
            strand: TxStrand::Plus,
            sequence: Some("ATGCGCTAA".to_string()),
            cds_start: Some(1), // 1-based inclusive per Transcript convention
            cds_end: Some(9),
            exons: vec![Exon::new(1, 1, 9)],
            chromosome: Some("chr1".to_string()),
            genomic_start: Some(1000),
            genomic_end: Some(1008),
            genome_build: Default::default(),
            mane_status: ManeStatus::default(),
            refseq_match: None,
            ensembl_match: None,
            exon_cigars: Vec::new(),
            cached_introns: OnceLock::new(),
        });
        // Genomic sequence: 999 N's + "ATGCGCTAA" + 100 N's.
        let prefix = "N".repeat(999);
        let suffix = "N".repeat(100);
        provider.add_genomic_sequence("chr1", format!("{}{}{}", prefix, "ATGCGCTAA", suffix));
        (projector, provider)
    }

    fn make_minus_strand_provider_and_projector() -> (Projector, MockProvider) {
        // Same 9bp CDS on chr1, but transcript is on the minus strand.
        let mut cdot = CdotMapper::new();
        cdot.add_transcript(
            "NM_TEST_MINUS.1".to_string(),
            CdotTranscript {
                gene_name: Some("TESTGENE".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Minus,
                exons: vec![[1000, 1009, 0, 9]],
                cds_start: Some(0),
                cds_end: Some(9),
                gene_id: None,
                protein: Some("NP_TEST_MINUS.1".to_string()),
                exon_cigars: Vec::new(),
            },
        );
        let projector = Projector::new(cdot);

        let mut provider = MockProvider::new();
        provider.add_transcript(Transcript {
            id: "NM_TEST_MINUS.1".to_string(),
            gene_symbol: Some("TESTGENE".to_string()),
            strand: TxStrand::Minus,
            sequence: Some("ATGCGCTAA".to_string()), // CDS as the transcript reads it
            cds_start: Some(1),                      // 1-based inclusive per Transcript convention
            cds_end: Some(9),
            exons: vec![Exon::new(1, 1, 9)],
            chromosome: Some("chr1".to_string()),
            genomic_start: Some(1000),
            genomic_end: Some(1008),
            genome_build: Default::default(),
            mane_status: ManeStatus::default(),
            refseq_match: None,
            ensembl_match: None,
            exon_cigars: Vec::new(),
            cached_introns: OnceLock::new(),
        });
        let prefix = "N".repeat(999);
        let suffix = "N".repeat(100);
        provider.add_genomic_sequence("chr1", format!("{}TTAGCGCAT{}", prefix, suffix));
        (projector, provider)
    }

    /// Build a two-transcript setup for project_all tests.
    ///
    /// NM_TX1.1: chr1 [1000,1009), plus strand, 9bp CDS "ATGCGCTAA"
    /// NM_TX2.1: chr1 [1000,1009), plus strand, 9bp CDS "ATGCGCTAA" (same region)
    ///           NM_TX2.1 is registered as MANE Select so it sorts first.
    fn make_two_transcript_setup() -> (Projector, MockProvider) {
        let mut cdot = CdotMapper::new();
        cdot.add_transcript(
            "NM_TX1.1".to_string(),
            CdotTranscript {
                gene_name: Some("GENE1".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Plus,
                exons: vec![[1000, 1009, 0, 9]],
                cds_start: Some(0),
                cds_end: Some(9),
                gene_id: None,
                protein: Some("NP_TX1.1".to_string()),
                exon_cigars: Vec::new(),
            },
        );
        cdot.add_transcript(
            "NM_TX2.1".to_string(),
            CdotTranscript {
                gene_name: Some("GENE1".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Plus,
                exons: vec![[1000, 1009, 0, 9]],
                cds_start: Some(0),
                cds_end: Some(9),
                gene_id: None,
                protein: Some("NP_TX2.1".to_string()),
                exon_cigars: Vec::new(),
            },
        );
        let projector = Projector::new(cdot)
            // Make NM_TX2.1 the MANE Select so it sorts first.
            .with_mane(vec!["NM_TX2.1".to_string()], vec![]);

        let mut provider = MockProvider::new();
        for id in ["NM_TX1.1", "NM_TX2.1"] {
            provider.add_transcript(Transcript {
                id: id.to_string(),
                gene_symbol: Some("GENE1".to_string()),
                strand: TxStrand::Plus,
                sequence: Some("ATGCGCTAA".to_string()),
                cds_start: Some(1),
                cds_end: Some(9),
                exons: vec![Exon::new(1, 1, 9)],
                chromosome: Some("chr1".to_string()),
                genomic_start: Some(1000),
                genomic_end: Some(1008),
                genome_build: Default::default(),
                mane_status: ManeStatus::default(),
                refseq_match: None,
                ensembl_match: None,
                exon_cigars: Vec::new(),
                cached_introns: OnceLock::new(),
            });
        }
        let prefix = "N".repeat(999);
        let suffix = "N".repeat(100);
        provider.add_genomic_sequence("chr1", format!("{}{}{}", prefix, "ATGCGCTAA", suffix));
        (projector, provider)
    }

    // -------------------------------------------------------------------------
    // Existing tests (preserved)
    // -------------------------------------------------------------------------

    #[test]
    fn project_substitution_minus_strand_revcomps_ref_alt() {
        let (projector, provider) = make_minus_strand_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("chr1:g.1005G>A", "NM_TEST_MINUS.1")
            .expect("minus-strand projection should succeed");
        let c = result
            .coding
            .as_ref()
            .expect("c. should be present")
            .to_string();
        assert!(
            c.contains(":c.4C>T"),
            "expected revcomp c.4C>T for minus strand, got: {}",
            c
        );
        let p = result
            .protein
            .as_ref()
            .expect("p. should be present")
            .to_string();
        assert_eq!(p, "NP_TEST_MINUS.1(TESTGENE):p.(Arg2Cys)");
        assert!(!result.is_frameshift);
        assert!(!result.is_intronic);
        assert!(!result.is_utr);
    }

    fn make_intronic_test_data() -> (Projector, MockProvider) {
        // Two-exon coding transcript on chr1, plus strand.
        //
        //   Exon 1: genome [1000, 1010), tx [0, 10)  — 10 bp
        //   Intron: genome [1010, 2000)               — 990 bp
        //   Exon 2: genome [2000, 2010), tx [10, 20) — 10 bp (last 2 are pad)
        //
        // CDS: tx [0, 18) → 18 bp → 6 codons: ATG-CGC-AAA-GGG-TAA-CCC
        //   (Met-Arg-Lys-Gly-Stop-Pro)
        //
        // Test position g.1015 is in the intron, 6 bases after the end of exon 1
        // (exon 1 ends at genome 1010, exclusive; last exonic base is g.1009;
        //  distance = 1015-1010+1 = 6).  Maps to c.9+6 or c.10+6 depending on
        // whether tx_end is inclusive or exclusive in the boundary calculation.
        let mut cdot = CdotMapper::new();
        cdot.add_transcript(
            "NM_INTR.1".to_string(),
            CdotTranscript {
                gene_name: Some("INTRGENE".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Plus,
                exons: vec![[1000, 1010, 0, 10], [2000, 2010, 10, 20]],
                cds_start: Some(0),
                cds_end: Some(18),
                gene_id: None,
                protein: Some("NP_INTR.1".to_string()),
                exon_cigars: Vec::new(),
            },
        );
        let projector = Projector::new(cdot);

        let mut provider = MockProvider::new();
        provider.add_transcript(Transcript {
            id: "NM_INTR.1".to_string(),
            gene_symbol: Some("INTRGENE".to_string()),
            strand: TxStrand::Plus,
            sequence: Some("ATGCGCAAAGGGTAACCC".to_string()), // 18 bp
            cds_start: Some(1),
            cds_end: Some(18),
            exons: vec![Exon::new(1, 1, 10), Exon::new(2, 11, 20)],
            chromosome: Some("chr1".to_string()),
            genomic_start: Some(1000),
            genomic_end: Some(2009),
            genome_build: Default::default(),
            mane_status: ManeStatus::default(),
            refseq_match: None,
            ensembl_match: None,
            exon_cigars: Vec::new(),
            cached_introns: OnceLock::new(),
        });
        let exon1 = "ATGCGCAAAG"; // 10 bp (genomic positions 1000..1009)
        let intron = "N".repeat(990); // genomic positions 1010..1999 (990 bp)
        let exon2 = "GGTAACCCNN"; // 10 bp pad (genomic positions 2000..2009)
        let prefix = "N".repeat(999);
        let suffix = "N".repeat(100);
        provider.add_genomic_sequence("chr1", format!("{prefix}{exon1}{intron}{exon2}{suffix}"));
        (projector, provider)
    }

    #[test]
    fn project_intronic_substitution_no_protein() {
        let (projector, provider) = make_intronic_test_data();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1015A>G", "NM_INTR.1")
            .expect("intronic substitution should project to c. with offset");
        assert!(result.is_intronic, "expected is_intronic=true");
        assert!(result.protein.is_none(), "no p. for intronic substitutions");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(
            c.contains('+'),
            "expected intronic offset notation (e.g. c.9+6 or c.10+6), got: {}",
            c
        );
    }

    #[test]
    fn project_no_overlap_returns_transcript_not_overlapping() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let err = vp
            .project("NC_000001.11:g.5000A>G", "NM_TEST.1")
            .expect_err("should fail to project outside the transcript");
        assert!(
            matches!(err, FerroError::TranscriptNotOverlapping { .. }),
            "expected TranscriptNotOverlapping, got: {:?}",
            err
        );
    }

    #[test]
    fn project_substitution_plus_strand_missense() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);

        let result = vp
            .project("chr1:g.1003C>A", "NM_TEST.1")
            .expect("projection should succeed");

        assert_eq!(result.transcript_id, "NM_TEST.1");
        assert_eq!(result.gene_symbol.as_deref(), Some("TESTGENE"));

        let c = result
            .coding
            .as_ref()
            .expect("c. should be present")
            .to_string();
        assert!(c.contains(":c.4C>A"), "expected ':c.4C>A' in '{}' ", c);

        let p = result
            .protein
            .as_ref()
            .expect("p. should be present")
            .to_string();
        assert_eq!(p, "NP_TEST.1(TESTGENE):p.(Arg2Ser)");

        assert!(!result.is_frameshift);
        assert!(!result.is_intronic);
        assert!(!result.is_utr);
    }

    #[test]
    fn project_single_base_deletion_is_frameshift() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1004del", "NM_TEST.1")
            .expect("deletion should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains(":c."), "expected c. variant, got: {}", c);
        assert!(c.contains("del"), "expected del notation in c., got: {}", c);
        let p = result
            .protein
            .as_ref()
            .expect("p. expected for CDS del")
            .to_string();
        assert!(p.contains("Arg2"), "expected Arg2 in p.: {}", p);
        assert!(p.contains("fs"), "expected fs in p.: {}", p);
        assert!(result.is_frameshift, "1-base del should be frameshift");
        assert!(!result.is_intronic);
    }

    #[test]
    fn project_three_base_deletion_in_frame() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1003_1005del", "NM_TEST.1")
            .expect("3-base del should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains("del"), "expected del notation, got: {}", c);
        let p = result
            .protein
            .as_ref()
            .expect("p. expected for in-frame del")
            .to_string();
        assert!(p.contains("Arg2del"), "expected Arg2del in p.: {}", p);
        assert!(!result.is_frameshift, "3-base deletion is in-frame");
    }

    #[test]
    fn project_single_base_insertion_is_frameshift() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1003_1004insA", "NM_TEST.1")
            .expect("insertion should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains("ins"), "expected ins notation, got: {}", c);
        assert!(result.protein.is_some(), "p. expected for CDS insertion");
        assert!(result.is_frameshift, "1-base insertion is frameshift");
    }

    #[test]
    fn project_duplication() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1004dup", "NM_TEST.1")
            .expect("dup should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains("dup"), "expected dup notation, got: {}", c);
        assert!(result.protein.is_some(), "p. expected for CDS dup");
        assert!(result.is_frameshift, "1-base dup is frameshift");
    }

    #[test]
    fn project_delins() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1003_1004delinsAT", "NM_TEST.1")
            .expect("delins should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains("delins"), "expected delins notation, got: {}", c);
        let p = result
            .protein
            .as_ref()
            .expect("p. expected for delins")
            .to_string();
        assert!(p.contains("delins"), "expected delins in p.: {}", p);
        assert!(
            !result.is_frameshift,
            "delins of equal length is not a frameshift"
        );
    }

    #[test]
    fn project_inversion() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("NC_000001.11:g.1003_1005inv", "NM_TEST.1")
            .expect("inv should project");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains("inv"), "expected inv notation, got: {}", c);
        let p = result
            .protein
            .as_ref()
            .expect("p. expected for inv")
            .to_string();
        assert!(p.contains("Arg2"), "expected Arg2 in p.: {}", p);
        assert!(p.contains("delins"), "expected delins in p.: {}", p);
        assert!(p.contains("Ala"), "expected Ala in p.: {}", p);
        assert!(!result.is_frameshift, "inversion is not a frameshift");
    }

    fn make_ensembl_provider_and_projector() -> (Projector, MockProvider) {
        // Same CDS as make_test_provider_and_projector but the transcript ID is
        // an Ensembl accession (no NM_/XM_ prefix) and cdot.protein is absent.
        // The projector must NOT fabricate a bogus protein accession via
        // substring substitution; it should skip protein prediction instead.
        let mut cdot = CdotMapper::new();
        cdot.add_transcript(
            "ENST00000000001.1".to_string(),
            CdotTranscript {
                gene_name: Some("TESTGENE".to_string()),
                contig: "chr1".to_string(),
                strand: ProvStrand::Plus,
                exons: vec![[1000, 1009, 0, 9]],
                cds_start: Some(0),
                cds_end: Some(9),
                gene_id: None,
                protein: None,
                exon_cigars: Vec::new(),
            },
        );
        let projector = Projector::new(cdot);

        let mut provider = MockProvider::new();
        provider.add_transcript(Transcript {
            id: "ENST00000000001.1".to_string(),
            gene_symbol: Some("TESTGENE".to_string()),
            strand: TxStrand::Plus,
            sequence: Some("ATGCGCTAA".to_string()),
            cds_start: Some(1),
            cds_end: Some(9),
            exons: vec![Exon::new(1, 1, 9)],
            chromosome: Some("chr1".to_string()),
            genomic_start: Some(1000),
            genomic_end: Some(1008),
            genome_build: Default::default(),
            mane_status: ManeStatus::default(),
            refseq_match: None,
            ensembl_match: None,
            exon_cigars: Vec::new(),
            cached_introns: OnceLock::new(),
        });
        let prefix = "N".repeat(999);
        let suffix = "N".repeat(100);
        provider.add_genomic_sequence("chr1", format!("{}{}{}", prefix, "ATGCGCTAA", suffix));
        (projector, provider)
    }

    #[test]
    fn project_substitution_no_protein_accession_skips_protein() {
        let (projector, provider) = make_ensembl_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let result = vp
            .project("chr1:g.1003C>A", "ENST00000000001.1")
            .expect("projection should succeed");
        let c = result.coding.as_ref().expect("c. expected").to_string();
        assert!(c.contains(":c.4C>A"), "expected c.4C>A, got: {}", c);
        // Neither NM_/XM_ prefix nor cdot.protein: must skip protein prediction.
        assert!(
            result.protein.is_none(),
            "expected no protein for accession with no NM_/XM_ prefix and no cdot.protein, got: {:?}",
            result.protein
        );
    }

    // -------------------------------------------------------------------------
    // project_normalized tests
    // -------------------------------------------------------------------------

    #[test]
    fn project_normalized_same_result_as_project_variant() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);

        let variant = crate::parse_hgvs("chr1:g.1003C>A").expect("parse should succeed");
        let via_project = vp
            .project_variant(&variant, "NM_TEST.1")
            .expect("project_variant should succeed");
        // Pre-normalize via the cached normalizer, then call project_normalized.
        let normalized = vp.normalizer.normalize(&variant).expect("normalize failed");
        let via_normalized = vp
            .project_normalized(&normalized, "NM_TEST.1")
            .expect("project_normalized should succeed");

        assert_eq!(
            via_project.coding.as_ref().map(|v| v.to_string()),
            via_normalized.coding.as_ref().map(|v| v.to_string()),
            "project_normalized should produce same c. as project_variant"
        );
        assert_eq!(
            via_project.protein.as_ref().map(|v| v.to_string()),
            via_normalized.protein.as_ref().map(|v| v.to_string()),
            "project_normalized should produce same p. as project_variant"
        );
    }

    // -------------------------------------------------------------------------
    // project_all / project_variant_all tests
    // -------------------------------------------------------------------------

    #[test]
    fn project_variant_all_returns_both_transcripts() {
        let (projector, provider) = make_two_transcript_setup();
        let vp = VariantProjector::new(projector, provider);

        let results = vp
            .project_all("chr1:g.1003C>A")
            .expect("project_all should succeed");

        assert_eq!(
            results.len(),
            2,
            "expected projections onto both transcripts, got: {}",
            results.len()
        );
    }

    #[test]
    fn project_all_mane_select_sorts_first() {
        let (projector, provider) = make_two_transcript_setup();
        let vp = VariantProjector::new(projector, provider);

        let results = vp
            .project_all("chr1:g.1003C>A")
            .expect("project_all should succeed");

        // NM_TX2.1 is MANE Select → must be first.
        assert_eq!(
            results[0].transcript_id, "NM_TX2.1",
            "MANE Select should be first"
        );
    }

    #[test]
    fn project_all_no_overlap_returns_empty() {
        let (projector, provider) = make_two_transcript_setup();
        let vp = VariantProjector::new(projector, provider);

        // g.5000 is far outside all transcripts.
        let results = vp
            .project_all("NC_000001.11:g.5000A>G")
            .expect("project_all should return Ok for no overlaps");

        assert!(
            results.is_empty(),
            "expected empty result for non-overlapping variant"
        );
    }

    // -------------------------------------------------------------------------
    // Allele compound projection tests
    // -------------------------------------------------------------------------

    /// Helper: build a cis allele `[chr1:g.1003C>A;chr1:g.1006T>A]` and
    /// project it onto NM_TEST.1.
    fn project_cis_allele() -> VariantProjection {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);

        // Use parse → project_variant to build the allele naturally.
        // g.1003 is C (c.4) and g.1006 is T (c.7) in the test fixture
        // "ATGCGCTAA"; using the correct ref bases keeps the test
        // valid HGVS rather than just exercising control flow.
        let v1 = crate::parse_hgvs("chr1:g.1003C>A").expect("v1 parse");
        let v2 = crate::parse_hgvs("chr1:g.1006T>A").expect("v2 parse");
        let allele = HgvsVariant::Allele(AlleleVariant::cis(vec![v1, v2]));
        vp.project_variant(&allele, "NM_TEST.1")
            .expect("cis allele projection should succeed")
    }

    #[test]
    fn project_cis_allele_produces_cis_coding_allele() {
        let result = project_cis_allele();
        let coding = result.coding.as_ref().expect("c. allele should be present");
        // The coding variant should itself be an Allele.
        assert!(
            matches!(coding, HgvsVariant::Allele(av) if av.phase == AllelePhase::Cis),
            "expected Cis coding allele, got: {}",
            coding
        );
        // Two inner c. variants.
        if let HgvsVariant::Allele(av) = coding {
            assert_eq!(
                av.variants.len(),
                2,
                "expected 2 inner c. variants in cis allele"
            );
        }
    }

    #[test]
    fn project_trans_allele_preserves_trans_phase() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);

        // Ref bases match the fixture: g.1003 = C, g.1006 = T.
        let v1 = crate::parse_hgvs("chr1:g.1003C>A").expect("v1 parse");
        let v2 = crate::parse_hgvs("chr1:g.1006T>A").expect("v2 parse");
        let allele = HgvsVariant::Allele(AlleleVariant::trans(vec![v1, v2]));
        let result = vp
            .project_variant(&allele, "NM_TEST.1")
            .expect("trans allele projection should succeed");

        let coding = result.coding.as_ref().expect("c. expected");
        assert!(
            matches!(coding, HgvsVariant::Allele(av) if av.phase == AllelePhase::Trans),
            "expected Trans coding allele, got: {}",
            coding
        );
    }

    #[test]
    fn project_allele_with_frameshift_inner_sets_is_frameshift() {
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);

        // g.1004del is a 1-base deletion → frameshift.
        let v1 = crate::parse_hgvs("chr1:g.1003C>A").expect("v1 parse");
        let v_fs = crate::parse_hgvs("NC_000001.11:g.1004del").expect("fs parse");
        let allele = HgvsVariant::Allele(AlleleVariant::cis(vec![v1, v_fs]));
        let result = vp
            .project_variant(&allele, "NM_TEST.1")
            .expect("allele with frameshift should project");

        assert!(
            result.is_frameshift,
            "allele containing a frameshift inner variant should set is_frameshift=true"
        );
    }

    #[test]
    fn project_allele_with_non_protein_inner_has_no_protein() {
        // An allele where one inner variant has no protein (intronic) →
        // the whole allele protein should be None.
        let (projector, provider) = make_intronic_test_data();
        let vp = VariantProjector::new(projector, provider);

        // g.1003 (exonic, ref C in NM_INTR.1 fixture) + g.1015 (intronic, ref N
        // since g.1015 is in the intron gap — the projector doesn't validate
        // intronic ref bases against the genomic reference).
        let v_exon = crate::parse_hgvs("NC_000001.11:g.1003C>G").expect("exon parse");
        let v_intron = crate::parse_hgvs("NC_000001.11:g.1015N>G").expect("intron parse");
        let allele = HgvsVariant::Allele(AlleleVariant::cis(vec![v_exon, v_intron]));
        let result = vp
            .project_variant(&allele, "NM_INTR.1")
            .expect("allele with intronic variant should project");

        assert!(
            result.protein.is_none(),
            "allele with intronic inner variant should have no protein"
        );
        assert!(result.is_intronic, "should be marked intronic");
    }

    #[test]
    fn project_empty_allele_unknown_transcript_returns_reference_not_found() {
        // Regression: the empty-allele fast path used to silently return Ok(...)
        // for any transcript_id, even one not present in the cdot mapper. That
        // was inconsistent with every other projection path, which surfaces
        // ReferenceNotFound for unknown accessions.
        let (projector, provider) = make_test_provider_and_projector();
        let vp = VariantProjector::new(projector, provider);
        let empty_allele = HgvsVariant::Allele(AlleleVariant::cis(vec![]));
        let err = vp
            .project_variant(&empty_allele, "NM_DOES_NOT_EXIST.1")
            .expect_err("empty allele on unknown transcript should error");
        assert!(
            matches!(err, FerroError::ReferenceNotFound { ref id } if id == "NM_DOES_NOT_EXIST.1"),
            "expected ReferenceNotFound for unknown transcript, got: {:?}",
            err
        );
    }
}