chore: release v0.7.0 by nh13 · Pull Request #633 · fulcrumgenomics/ferro-hgvs

nh13 · 2026-06-13T22:01:41Z

🤖 New release

ferro-hgvs: 0.6.0 -> 0.7.0 (⚠ API breaking changes)

⚠ `ferro-hgvs` breaking changes

--- failure constructible_struct_adds_field: externally-constructible struct adds field ---

Description:
A pub struct constructible with a struct literal has a new pub field. Existing struct literals must be updated to include the new field.
        ref: https://doc.rust-lang.org/reference/expressions/struct-expr.html
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/constructible_struct_adds_field.ron

Failed in:
  field CdsPos.special in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/location.rs:147
  field CdsPos.special in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/location.rs:147
  field BiocommonsLocalConfig.uta_ready_timeout_secs in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/biocommons.rs:47
  field BiocommonsLocalConfig.uta_ready_timeout_secs in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/biocommons.rs:47
  field AppState.reference in /tmp/.tmptrMAuu/ferro-hgvs/src/service/server.rs:73
  field VariantProjection.noncoding in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:27
  field VariantProjection.rna in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:32
  field VariantProjection.affects_init in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:49
  field VariantProjection.noncoding in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:27
  field VariantProjection.rna in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:32
  field VariantProjection.affects_init in /tmp/.tmptrMAuu/ferro-hgvs/src/project/result.rs:49
  field ReferenceManifest.protein_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:20
  field ReferenceManifest.refseqgene_alignments in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:33
  field ReferenceManifest.refseqgene_alignments_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:39
  field ReferenceManifest.assembly_report in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:44
  field ReferenceManifest.assembly_report_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:48
  field ReferenceManifest.derived_refseqgene_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:56
  field ReferenceManifest.ng_hosted_transcripts in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:60
  field ReferenceManifest.derived_transcript_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:66
  field ReferenceManifest.refseqgene_summary in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:71
  field ReferenceManifest.ensembl_cdot_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:89
  field ReferenceManifest.ensembl_cdot_grch37_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:92
  field ReferenceManifest.ensembl_transcript_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:96
  field ReferenceManifest.backfill_transcripts_fasta in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:107
  field ReferenceManifest.canonical_overrides in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:125
  field ReferenceManifest.protein_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:20
  field ReferenceManifest.refseqgene_alignments in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:33
  field ReferenceManifest.refseqgene_alignments_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:39
  field ReferenceManifest.assembly_report in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:44
  field ReferenceManifest.assembly_report_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:48
  field ReferenceManifest.derived_refseqgene_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:56
  field ReferenceManifest.ng_hosted_transcripts in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:60
  field ReferenceManifest.derived_transcript_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:66
  field ReferenceManifest.refseqgene_summary in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:71
  field ReferenceManifest.ensembl_cdot_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:89
  field ReferenceManifest.ensembl_cdot_grch37_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:92
  field ReferenceManifest.ensembl_transcript_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:96
  field ReferenceManifest.backfill_transcripts_fasta in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:107
  field ReferenceManifest.canonical_overrides in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:125
  field ReferenceManifest.protein_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:20
  field ReferenceManifest.refseqgene_alignments in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:33
  field ReferenceManifest.refseqgene_alignments_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:39
  field ReferenceManifest.assembly_report in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:44
  field ReferenceManifest.assembly_report_grch37 in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:48
  field ReferenceManifest.derived_refseqgene_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:56
  field ReferenceManifest.ng_hosted_transcripts in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:60
  field ReferenceManifest.derived_transcript_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:66
  field ReferenceManifest.refseqgene_summary in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:71
  field ReferenceManifest.ensembl_cdot_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:89
  field ReferenceManifest.ensembl_cdot_grch37_json in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:92
  field ReferenceManifest.ensembl_transcript_fastas in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:96
  field ReferenceManifest.backfill_transcripts_fasta in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:107
  field ReferenceManifest.canonical_overrides in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/manifest.rs:125
  field AlleleVariant.uncertain in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:574
  field AlleleVariant.uncertain in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:574
  field ValidateResponse.wraps_origin in /tmp/.tmptrMAuu/ferro-hgvs/src/service/types.rs:546
  field ValidateResponse.wraps_origin in /tmp/.tmptrMAuu/ferro-hgvs/src/service/types.rs:546
  field PrepareConfig.download_proteins in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:40
  field PrepareConfig.download_ensembl in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:55
  field PrepareConfig.validate_canonical_accessions in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:65
  field PrepareConfig.derive_ng_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:68
  field PrepareConfig.backfill_transcripts in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:75
  field PrepareConfig.genome in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:78
  field PrepareConfig.download_proteins in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:40
  field PrepareConfig.download_ensembl in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:55
  field PrepareConfig.validate_canonical_accessions in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:65
  field PrepareConfig.derive_ng_placements in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:68
  field PrepareConfig.backfill_transcripts in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:75
  field PrepareConfig.genome in /tmp/.tmptrMAuu/ferro-hgvs/src/prepare/mod.rs:78

--- failure enum_marked_non_exhaustive: enum marked #[non_exhaustive] ---

Description:
A public enum has been marked #[non_exhaustive]. Pattern-matching on it outside of its crate must now include a wildcard pattern like `_`, or it will fail to compile.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#attr-adding-non-exhaustive
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_marked_non_exhaustive.ron

Failed in:
  enum NormalizationWarning in /tmp/.tmptrMAuu/ferro-hgvs/src/normalize/mod.rs:394

--- failure enum_no_repr_variant_discriminant_changed: enum variant had its discriminant change value ---

Description:
The enum's variant had its discriminant value change. This breaks downstream code that used its value via a numeric cast like `as isize`.
        ref: https://doc.rust-lang.org/reference/items/enumerations.html#assigning-discriminant-values
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_no_repr_variant_discriminant_changed.ron

Failed in:
  variant ProteinEdit::Deletion 1 -> 2 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1079
  variant ProteinEdit::Insertion 2 -> 3 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1087
  variant ProteinEdit::Delins 3 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1090
  variant ProteinEdit::Duplication 4 -> 5 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1093
  variant ProteinEdit::Frameshift 5 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1096
  variant ProteinEdit::Extension 6 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1115
  variant ProteinEdit::Identity 7 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1123
  variant ProteinEdit::Unknown 8 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1132
  variant ProteinEdit::NoProtein 9 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1141
  variant ProteinEdit::Repeat 10 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1149
  variant ProteinEdit::MultiRepeat 11 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1158
  variant ProteinEdit::Deletion 1 -> 2 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1079
  variant ProteinEdit::Insertion 2 -> 3 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1087
  variant ProteinEdit::Delins 3 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1090
  variant ProteinEdit::Duplication 4 -> 5 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1093
  variant ProteinEdit::Frameshift 5 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1096
  variant ProteinEdit::Extension 6 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1115
  variant ProteinEdit::Identity 7 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1123
  variant ProteinEdit::Unknown 8 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1132
  variant ProteinEdit::NoProtein 9 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1141
  variant ProteinEdit::Repeat 10 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1149
  variant ProteinEdit::MultiRepeat 11 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1158
  variant ErrorType::SingleLetterAminoAcid 6 -> 5 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:88
  variant ErrorType::WrongQuoteCharacter 7 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:91
  variant ErrorType::LowercaseAccessionPrefix 8 -> 7 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:94
  variant ErrorType::MixedCaseEditType 9 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:97
  variant ErrorType::OldSubstitutionSyntax 10 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:100
  variant ErrorType::InvalidUnicodeCharacter 11 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:103
  variant ErrorType::SwappedPositions 12 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:106
  variant ErrorType::TrailingAnnotation 13 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:113
  variant ErrorType::MissingCoordinatePrefix 14 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:119
  variant ErrorType::OldAlleleFormat 15 -> 14 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:127
  variant ErrorType::DeprecatedStopCodonStar 16 -> 15 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:134
  variant ErrorType::DeprecatedStopCodonX 17 -> 16 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:143
  variant ErrorType::DeprecatedFrameshiftStar 18 -> 17 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:151
  variant ErrorType::DeprecatedFrameshiftX 19 -> 18 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:158
  variant ErrorType::DelSizeSuffix 20 -> 19 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:166
  variant ErrorType::EmptyDelinsInsert 21 -> 20 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:174
  variant ErrorType::RedundantRepeatLabel 22 -> 21 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:182
  variant ErrorType::SinglePositionRange 23 -> 22 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:192
  variant ErrorType::RefSeqMismatch 24 -> 23 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:203
  variant ErrorType::DeprecatedIvsNotation 25 -> 24 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:212
  variant ErrorType::DeprecatedConSyntax 26 -> 25 in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:219
  variant NaEdit::Insertion 3 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:563
  variant NaEdit::Delins 4 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:582
  variant NaEdit::Duplication 5 -> 7 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:589
  variant NaEdit::DupIns 6 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:599
  variant NaEdit::Inversion 7 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:602
  variant NaEdit::Repeat 8 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:612
  variant NaEdit::MultiRepeat 9 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:624
  variant NaEdit::Identity 10 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:631
  variant NaEdit::Conversion 11 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:639
  variant NaEdit::Unknown 12 -> 14 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:646
  variant NaEdit::Methylation 13 -> 15 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:652
  variant NaEdit::CopyNumber 14 -> 16 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:655
  variant NaEdit::Splice 15 -> 17 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:671
  variant NaEdit::NoProduct 16 -> 18 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:675
  variant NaEdit::PositionOnly 17 -> 19 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:680
  variant NaEdit::Insertion 3 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:563
  variant NaEdit::Delins 4 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:582
  variant NaEdit::Duplication 5 -> 7 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:589
  variant NaEdit::DupIns 6 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:599
  variant NaEdit::Inversion 7 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:602
  variant NaEdit::Repeat 8 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:612
  variant NaEdit::MultiRepeat 9 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:624
  variant NaEdit::Identity 10 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:631
  variant NaEdit::Conversion 11 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:639
  variant NaEdit::Unknown 12 -> 14 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:646
  variant NaEdit::Methylation 13 -> 15 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:652
  variant NaEdit::CopyNumber 14 -> 16 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:655
  variant NaEdit::Splice 15 -> 17 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:671
  variant NaEdit::NoProduct 16 -> 18 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:675
  variant NaEdit::PositionOnly 17 -> 19 in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:680
  variant FerroError::ExonIntronBoundary 2 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:369
  variant FerroError::UtrCdsBoundary 3 -> 5 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:373
  variant FerroError::InvalidCoordinates 4 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:377
  variant FerroError::UnsupportedVariant 5 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:390
  variant FerroError::IntronicVariant 6 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:401
  variant FerroError::GenomicReferenceNotAvailable 7 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:408
  variant FerroError::ProteinReferenceNotAvailable 8 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:416
  variant FerroError::AminoAcidMismatch 9 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:424
  variant FerroError::ReferenceMismatch 10 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:433
  variant FerroError::ConversionError 11 -> 15 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:457
  variant FerroError::TranscriptNotOverlapping 12 -> 16 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:461
  variant FerroError::ProteinSequenceUnavailable 13 -> 17 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:468
  variant FerroError::UnsupportedProjection 14 -> 18 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:472
  variant FerroError::Io 15 -> 19 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:476
  variant FerroError::Json 16 -> 20 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:480
  variant FerroError::ExonIntronBoundary 2 -> 4 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:369
  variant FerroError::UtrCdsBoundary 3 -> 5 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:373
  variant FerroError::InvalidCoordinates 4 -> 6 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:377
  variant FerroError::UnsupportedVariant 5 -> 8 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:390
  variant FerroError::IntronicVariant 6 -> 9 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:401
  variant FerroError::GenomicReferenceNotAvailable 7 -> 10 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:408
  variant FerroError::ProteinReferenceNotAvailable 8 -> 11 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:416
  variant FerroError::AminoAcidMismatch 9 -> 12 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:424
  variant FerroError::ReferenceMismatch 10 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:433
  variant FerroError::ConversionError 11 -> 15 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:457
  variant FerroError::TranscriptNotOverlapping 12 -> 16 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:461
  variant FerroError::ProteinSequenceUnavailable 13 -> 17 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:468
  variant FerroError::UnsupportedProjection 14 -> 18 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:472
  variant FerroError::Io 15 -> 19 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:476
  variant FerroError::Json 16 -> 20 in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:480
  variant DiagnosticPayload::Other 12 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/reference/annotation/diagnostics.rs:66
  variant DiagnosticPayload::Other 12 -> 13 in /tmp/.tmptrMAuu/ferro-hgvs/src/reference/annotation/diagnostics.rs:66

--- failure enum_struct_variant_field_added: pub enum struct variant field added ---

Description:
An enum's exhaustive struct variant has a new field, which has to be included when constructing or matching on this variant.
        ref: https://doc.rust-lang.org/reference/attributes/type_system.html#the-non_exhaustive-attribute
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_struct_variant_field_added.ron

Failed in:
  field uta_ready_timeout_secs of variant SetupCommands::Uta in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/cli.rs:705
  field base of variant DelinsSubedit::IdentityAt in /tmp/.tmptrMAuu/ferro-hgvs/src/normalize/rules.rs:910
  field details of variant NormalizationWarning::RefSeqMismatch in /tmp/.tmptrMAuu/ferro-hgvs/src/normalize/mod.rs:423
  field detail of variant FerroError::IntronicVariant in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:403
  field detail of variant FerroError::IntronicVariant in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:403
  field ter of variant ProteinEdit::Frameshift in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1100
  field ter of variant ProteinEdit::Frameshift in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1100

--- failure enum_struct_variant_field_missing: pub enum struct variant's field removed or renamed ---

Description:
A publicly-visible enum has a struct variant whose field is no longer available under its prior name. It may have been renamed or removed entirely.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#item-remove
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_struct_variant_field_missing.ron

Failed in:
  field ter_pos of variant ProteinEdit::Frameshift, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/hgvs/edit.rs:931
  field ter_pos of variant ProteinEdit::Frameshift, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/hgvs/edit.rs:931
  field message of variant NormalizationWarning::RefSeqMismatch, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/mod.rs:82
  field message of variant NormalizationWarning::OverlapConflict, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/mod.rs:99

--- failure enum_variant_added: enum variant added on exhaustive enum ---

Description:
A publicly-visible enum without #[non_exhaustive] has a new variant.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#enum-variant-new
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_variant_added.ron

Failed in:
  variant HgvsVariant:GenomeRing in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1733
  variant HgvsVariant:Supernumerary in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1747
  variant HgvsVariant:GenomeRing in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1733
  variant HgvsVariant:Supernumerary in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1747
  variant HgvsVariant:GenomeRing in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1733
  variant HgvsVariant:Supernumerary in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:1747
  variant RepeatCount:UncertainRange in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:154
  variant ErrorCode:CoordinateSystemMismatch in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:38
  variant ErrorCode:TranscriptVersionNotExact in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:48
  variant ErrorCode:TranscriptSequenceUnreconstructable in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:52
  variant ErrorCode:AlignmentGap in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:68
  variant ErrorCode:AlleleFractionAnnotation in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:96
  variant ErrorCode:ClinVarProseMultiAllelic in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:98
  variant InsertedSequence:UncertainRangeInv in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:235
  variant InsertedSequence:SpecialPositionRange in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:246
  variant AllelePhase:AndOr in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:528
  variant AllelePhase:Products in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:534
  variant AllelePhase:AndOr in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:528
  variant AllelePhase:Products in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:534
  variant FerroError:TranscriptVersionNotExact in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:344
  variant FerroError:TranscriptSequenceUnreconstructable in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:365
  variant FerroError:AlignmentGap in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:386
  variant FerroError:VariantExceedsReference in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:447
  variant FerroError:TranscriptVersionNotExact in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:344
  variant FerroError:TranscriptSequenceUnreconstructable in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:365
  variant FerroError:AlignmentGap in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:386
  variant FerroError:VariantExceedsReference in /tmp/.tmptrMAuu/ferro-hgvs/src/error.rs:447
  variant ProteinEdit:SubstitutionAlternatives in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1076
  variant ProteinEdit:FrameshiftAlternatives in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1107
  variant ProteinEdit:SubstitutionAlternatives in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1076
  variant ProteinEdit:FrameshiftAlternatives in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:1107
  variant ErrorType:LengthMismatch in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:230
  variant ErrorType:AlleleFractionAnnotation in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:241
  variant ErrorType:ClinVarProseMultiAllelic in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:254
  variant ErrorType:RnaThymineCanonicalized in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:262
  variant ErrorType:NonSpecMosaicForm in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:272
  variant ErrorType:ProteinBracketedAaInsertion in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:283
  variant ErrorType:InitiatorMetCanonicalization in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:298
  variant ErrorType:DupSizeSuffix in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:308
  variant ErrorType:DupExplicitSeq in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:318
  variant ErrorType:DelExplicitSeq in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:328
  variant ErrorType:VariantExceedsReference in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:342
  variant ErrorType:UnresolvableCentromere in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:353
  variant ErrorType:TranscriptFlankNotDescribable in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:362
  variant ErrorType:PositionPastEnd in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:380
  variant ErrorType:OverlapConflictingEdits in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:395
  variant ErrorType:NonConformantBracketCardinality in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:418
  variant ErrorType:IntronicOnBareTranscript in /tmp/.tmptrMAuu/ferro-hgvs/src/error_handling/types.rs:433
  variant BenchmarkCommands:Matrix in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/cli.rs:543
  variant DiagnosticPayload:ConflictingProteinId in /tmp/.tmptrMAuu/ferro-hgvs/src/reference/annotation/diagnostics.rs:62
  variant DiagnosticPayload:ConflictingProteinId in /tmp/.tmptrMAuu/ferro-hgvs/src/reference/annotation/diagnostics.rs:62
  variant NaEdit:NPaddedDeletion in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:560
  variant NaEdit:BreakpointInsertion in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:570
  variant NaEdit:NPaddedDeletion in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:560
  variant NaEdit:BreakpointInsertion in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/edit.rs:570
  variant PyErrorType:LengthMismatch in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2396
  variant PyErrorType:AlleleFractionAnnotation in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2397
  variant PyErrorType:ClinVarProseMultiAllelic in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2398
  variant PyErrorType:RnaThymineCanonicalized in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2405
  variant PyErrorType:ProteinBracketedAaInsertion in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2406
  variant PyErrorType:PositionPastEnd in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2407
  variant PyErrorType:VariantExceedsReference in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2408
  variant PyErrorType:NonSpecMosaicForm in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2409
  variant PyErrorType:OverlapConflictingEdits in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2410
  variant PyErrorType:InitiatorMetCanonicalization in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2411
  variant PyErrorType:DupSizeSuffix in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2414
  variant PyErrorType:DupExplicitSeq in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2415
  variant PyErrorType:DelExplicitSeq in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2416
  variant PyErrorType:NonConformantBracketCardinality in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2420
  variant PyErrorType:UnresolvableCentromere in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2423
  variant PyErrorType:TranscriptFlankNotDescribable in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2426
  variant PyErrorType:IntronicOnBareTranscript in /tmp/.tmptrMAuu/ferro-hgvs/src/python.rs:2430

--- failure enum_variant_missing: pub enum variant removed or renamed ---

Description:
A publicly-visible enum has at least one variant that is no longer available under its prior name. It may have been renamed or removed entirely.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#item-remove
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/enum_variant_missing.ron

Failed in:
  variant ErrorType::PositionZero, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/error_handling/types.rs:83
  variant PyErrorType::PositionZero, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/python.rs:1932

--- failure function_missing: pub fn removed or renamed ---

Description:
A publicly-visible function cannot be imported by its prior path. A `pub use` may have been removed, or the function itself may have been renamed or removed entirely.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#item-remove
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/function_missing.ron

Failed in:
  function ferro_hgvs::normalize::rules::decompose_delins_inv, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/rules.rs:693
  function ferro_hgvs::benchmark::check_docker_available, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/benchmark/biocommons.rs:100
  function ferro_hgvs::python_helpers::edit_type_from_debug, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/python_helpers.rs:85

--- failure function_parameter_count_changed: pub fn parameter count changed ---

Description:
A publicly-visible function now takes a different number of parameters.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#fn-change-arity
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/function_parameter_count_changed.ron

Failed in:
  ferro_hgvs::normalize::rules::normalize_repeat now takes 6 parameters instead of 5, in /tmp/.tmptrMAuu/ferro-hgvs/src/normalize/rules.rs:1539
  ferro_hgvs::benchmark::biocommons::check_uta_local now takes 2 parameters instead of 1, in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/biocommons.rs:350
  ferro_hgvs::benchmark::check_uta_local now takes 2 parameters instead of 1, in /tmp/.tmptrMAuu/ferro-hgvs/src/benchmark/biocommons.rs:350

--- failure inherent_method_missing: pub method removed or renamed ---

Description:
A publicly-visible method or associated fn is no longer available under its prior name. It may have been renamed or removed entirely.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#item-remove
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/inherent_method_missing.ron

Failed in:
  Normalizer::normalize_with_warnings, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/mod.rs:229
  Normalizer::normalize_with_warnings, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/mod.rs:229

--- failure method_parameter_count_changed: pub method parameter count changed ---

Description:
A publicly-visible method now takes a different number of parameters, not counting the receiver (self) parameter.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#fn-change-arity
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/method_parameter_count_changed.ron

Failed in:
  ferro_hgvs::hgvs::variant::AlleleVariant::try_new_validated takes 2 parameters in /tmp/.tmpdj150K/ferro-hgvs/src/hgvs/variant.rs:565, but now takes 3 parameters in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:699
  ferro_hgvs::hgvs::AlleleVariant::try_new_validated takes 2 parameters in /tmp/.tmpdj150K/ferro-hgvs/src/hgvs/variant.rs:565, but now takes 3 parameters in /tmp/.tmptrMAuu/ferro-hgvs/src/hgvs/variant.rs:699

--- failure struct_missing: pub struct removed or renamed ---

Description:
A publicly-visible struct cannot be imported by its prior path. A `pub use` may have been removed, or the struct itself may have been renamed or removed entirely.
        ref: https://doc.rust-lang.org/cargo/reference/semver.html#item-remove
       impl: https://github.com/obi1kenobi/cargo-semver-checks/tree/v0.48.0/src/lints/struct_missing.ron

Failed in:
  struct ferro_hgvs::normalize::NormalizeResultWithWarnings, previously in file /tmp/.tmpdj150K/ferro-hgvs/src/normalize/mod.rs:131

Changelog

0.7.0 - 2026-07-02

Added

(python) normalize project_to_genomic output by default; raw via normalize=False (#888)

(project) NG_/LRG in-place c./n.→g. projection for compound alleles and UTR coordinates (#881)

(project) predict C-terminal extension / stop-loss for CDS→3'UTR-spanning deletion (#880)

(reference) provision NM_002001.2 conformance rows (#802) (#849)

(prepare) version-aware transcript backfill (#842) (#848)

(service/effect) real amino-acid resolution and junction-based NMD (#837)

(vcf) RNA→VCF conversion and complex-allele decomposition (#822)

(vcf) parse per-sample FORMAT genotype values (#823)

(project) translate downstream variants on non-AUG-initiation transcripts (#780) (#796)

(reference) provision exon→genome structure for cdot-absent old transcript versions (NM_003002.2) (#790) (#795)

(project) resolve legacy GENE_vNNN selectors on NG_(...):c./n./r. projection (#784)

(project) predict p.? for an initiation-codon member of a cis compound allele (#778)

(normalize) expand r. (RNA) cross-reference insert/delins payloads (#777)

(normalize) expand axis-less cross-reference insert payloads (#769)

(project) predict protein consequence for whole-exon deletions (#761)

(conformance) corpus-driven NG_ placement derivation (#744) (#747)

(conformance) hermetic genomic-axis PR gate (#737) (#746)

(prepare) produce derived_refseqgene_placements via --derive-ng-placements (#740) (#743)

(project) emit the g. axis for NG/LRG/NC-parent c.pter/c.qter inputs (#537) (#739)

(conformance) hermetic protein-axis PR gate (#719) (#733)

(conformance) hermetic snapshot-backed normalized-axis PR gate (feat(conformance): pinned, version-exact reference snapshot for a hermetic conformance gate #719 I4) (#729)

(reference) provision derived NG_ placements — load + produce (#728) (#732)

(reference) derive version-independent NG_ genomic placement — core (#728) (#731)

(conformance) pinned version-exact transcript reference snapshot (feat(conformance): pinned, version-exact reference snapshot for a hermetic conformance gate #719 I2) (#727)

(normalize,project) resolve legacy gene-model selectors on genomic references (#709)

(reference) cross-build version-exact cdot fallback for c. normalization (#720)

(project) curate project_*_all enumeration — collapse superseded versions, prefer curated transcripts (#710)

(project,python) --assembly genome-build override for build-agnostic NG_/LRG_ inputs (#723)

(reference,project) bundle GRCh37 RefSeqGene alignment + thread build through projection (#721)

(reference) build-aware NG_/LRG_ genomic placement (GRCh37 + GRCh38) foundation (#711)

(conformance) add reference-gap report tool (#722)

(cli,project) ferro project --axis {g,c,n,p,r} multi-axis projection surface (#712)

(conformance) add corpus accession inventory (#707)

(conformance) add reference_unavailable disposition (#706)

(project) add c.→r. RNA consequence prediction surface (#701)

(normalize) apply the 3′ rule across exon/intron boundaries (#670) (#700)

(normalize) emit the NP_ protein-accession selector for p. on genomic references (#502) (#676)

(prepare) add Ensembl reference support (ENST/ENSG/ENSP) (#677)

(check) validate CDS start-codon consistency in ferro check (#629) (#674)

(normalize) collapse overlapping cis-allele edits into a single delins (#667)

(project) extend the direct c.→p. path to bare n./r. transcript inputs (#506) (#661)

(project) enumerate + frame c./n./r. inputs with NG_/LRG_ context (#646) (#647)

(project) project NG_/LRG_ genomic inputs onto transcripts (#498) (#642)

(project) re-anchor NG_/LRG_-parent projections into the parent frame (#480) (#616)

(benchmark) perf-matrix engine + measured performance tables (#617)

(parser) parse and/or between bracketed alleles (#544) (#563)

(parser) parse predicted compound cis allele [(a;b)] (#545) (#569)

(parser) parse trans alleles with a mosaic (;) tail (#544) (#559)

(perf-table) render README performance tables from a results JSON (#604)

(reference) load + index the GRCh37 cdot so multi-build manifests project GRCh37 inputs (#605)

(error) emit AlignmentGap (E3007) for variants in a transcript-genome CIGAR indel (Cycle 1c-iii) (#603)

(parser) parse N-padded deletion over an uncertain range (#545) (#568)

(parser) parse comma products allele [a,b] (#545) (#571)

(parser) parse positionless breakpoint insertion in composite alleles (#546) (#584)

(tool-support) single source of truth for the tool-comparison tables (#590)

(parser) parse the sup supernumerary marker (#546) (#596)

(parser) accept pter/qter endpoints in inserted position-ranges (#546) (#597)

(parser) parse same-chromosome ring :: deletion-join (#546) (#595)

(parser) support inverted insertion of an uncertain-boundary range (#546) (#576)

(parser) accept all-identity trans alleles via cross-spell check (#544) (#558)

(project) add the c↔n (non-coding transcript) axis to VariantProjection (#592)

(parser) parse shared-position repeat trans alleles (#544) (#555)

(parser) parse predicted-wrapper members in protein alleles (#544) (#552)

(parser) parse residue-level and/or ^ substitutions (#544) (#550)

(parser) parse frameshift with alternative new residues (#544) (#557)

(parser) parse trans alleles whose members are cis groups (#544) (#549)

(parser) extend mosaic =/ to protein + fix RNA case (#544) (#548)

(parser) parse the and/or ^ operator (#544) (#547)

(conformance) generate failure-patterns.md from cases.json; retire hand-maintained counts (#509) (#538)

(reference) reconcile cdot for synthesis-only transcripts via exon-sum length (#520) (#532)

(reference) ingest protein FASTAs + get_protein_sequence + translation check (#520) (#530)

(reference) apply canonical overrides in MultiFastaProvider + reconcile cdot (#520) (#528)

(prepare) canonical-overrides acquisition — ferro prepare --validate-canonical (#520) (#527)

(normalize) resolve bare-transcript c. pter/qter telomere markers (fix(normalize): subtract-with-overflow panics on intronic/pter inputs #488 Phase 2) (#533)

(reference) version-exact correction of transcript metadata (#520) (#524)

(reference) offline structural validation of transcript records (#520) (#521)

(normalize) resolve genomic pter/qter telomere markers to concrete coordinates (#488) (#526)

(project) direct c.→p. path for bare-NM_ inputs; demote 4 bare-NP protein rows (#498) (#508)

(reference) strict exact-version transcript resolution (docs(test): design — annotated, self-correcting, hermetic conformance harness #478 pillar 3) (#490)

(error-handling) reject standalone single-member allele brackets uniformly (W3026, closes Enforce HGVS bracket/allele cardinality uniformly across all coordinate systems (strict mode) #493) (#496)

(error-handling) add W3023/W3024/W3025 for dup/dup/del soft-prohibition forms (closes parser: detect 'dup<N>', 'dup<seq>', 'del<seq>' soft-prohibition forms (W30xx) #460) (#462)

(parser) accept whole-entity edits in protein bracket members (closes parser: extend protein bracket-member dispatch to whole-entity edits (p.[=];[X]) (PR #433 follow-up) #468) (#475)

(normalize) expand ins[ACC:g.A_B] cross-reference to flat literal (closes normalize: expand ins[ACC:g.A_B] cross-reference to flat literal (#395 item 2 follow-up) #422) (#437)

(normalize) canonicalize p.delins → p.dup and surface W3022 InitiatorMetCanonicalization (closes p.ins → p.dup canonicalization #92) (#407)

contig-length-aware math + wraparound boundary policies for m./o. variants (closes normalize/parse/convert: contig-length-aware math + boundary policies for m./o. wraparound (#129 follow-up) #399) (#411)

(normalize,project,python,validate) four misc gaps from normalize: 6 misc gaps — repeat resumption, cross-ref ins, RNA U→T, Python warning surface, W5002 strict mode #395 (items 1, 4, 5, 6) (#421)

(parser) spec-compliant wraparound ranges on m./o. circular refs (#380)

(normalize) protein 3'-shifting for deletions and duplications (#377)

(normalize) expand ins[...] to flat literal sequence (closes feat(normalize): expand ins[...] (bracketed + reference-range) to flat literal #333) (#365)

(normalize) structured info-code surface mirroring W#### warnings (#373)

(project) VariantProjector accepts c./n./r. inputs (#379)

(error_handling) mutalyzer ↔ ferro error-code mapping table (closes feat(error_handling): mutalyzer ↔ ferro error-code mapping table #329) (#362)

(error-handling) W5003 VariantExceedsReference, strict-mode rejection (closes normalize: alignment-block-aware canonical split for delins crossing alignment gaps #355) (#363)

(test/mutalyzer-normalize) accepted_divergence + spec_citation (closes feat(test/mutalyzer-normalize): comparator support for accepted_divergence + spec_citation #335) (#359)

(parser) canonicalize r. thymine input to u with W3020 soft-warning (closes parser(rna): decide and pin r. thymine policy — reject t or canonicalize to u (#81 E follow-up to #232) #282) (#299)

(parser) recognize non-human Ensembl accession prefixes (#320)

(project) project_to_genomic for c./n./r. inputs (closes feat(project): expose c./n. → g. projection in VariantProjector #327) (#358)

(parser) RNA/TX trans-allele predicted-edit wrapper in compound brackets (closes parser: predicted-edit wrapper inside compound brackets for RNA / TX trans-allele parsers (follow-up to #244) #287) (#309)

(parser) whole-entity predicted forms for m./o./n. variants (closes parser: whole-entity predicted forms m.(=), m.(?), o.(=), n.(=) (follow-up to #246) #288) (#308)

(normalize) MultiRepeat partial validation for non-Exact counts (closes normalize(repeat): partial-validation mode for MultiRepeat with Range/Unknown counts (follow-up to #215) #279) (#296)

(annotation) populate Transcript.protein_id from GFF/GTF attributes (#321)

(parser) whole-entity predicted forms c.(=), c.(?), r.(=), r.(?), r.(0) (closes parser: whole-entity predicted forms c.(=), c.(?), r.(=), r.(?), r.(0) (follow-up to #241) #245) (#246)

(parser) predicted-edit wrapper inside compound brackets (closes parser: compound brackets with uncertain edit c.[(123A>G);125C>T] not yet supported (follow-up to #241) #243) (#244)

(parser) accept ?con and ?copy on unknown position (closes parser: ?con<src> / ?copy<N> with uncertain position — spec-questionable, currently rejected (follow-up to #240) #286) (#303)

(parser) bracket-aware split for chimeric + non-compact mosaic forms (closes Chimeric (//) round-trip + non-compact mosaic forms — audit and pin gaps #216) (#217)

(normalize) validate repeat unit divides reference span and matches bases (closes Repeat unit length must divide reference span and bases must match unit*N (normalize-time consistency check) #214) (#215)

Fixed

(project) cis-sort minus-strand compound-allele members on the project_variant genomic axis (#894) (#898)

(project) de-anchor bare NG_/LRG_ genomic input on the single-transcript projection paths (#879) (#896)

(project) surface the genomic axis for LRG inputs and pter/qter termini on project_variant (fix(project): project_variant returns genomic=None for LRG transcript inputs (raw pivot resolves) #886, fix(project): project_variant errors on pter/qter/cen position sentinels (raw pivot resolves) #887) (#893)

(normalize) keep out-of-phase insertions as ins, not spurious dup/repeat (#882) (#892)

(normalize) 3'-align insertion→duplication; guarantee normalization idempotency (#883)

(project) preserve LRG_t/LRG_p namespace on projection output (#860) (#874)

render in-frame single-codon deletion in a residue run as del, not empty ins (#850)

(project) spec-canonical minus-strand genomic repeat projection (#852) (#869)

(parser) collapse single-element bracketed literal ins/delins to a plain literal (#863)

(project) canonicalize protein consequences (delins→sub, tandem dup, adjacent in-cis delins) (#862)

(project) build-scope the predicted-r. allele transcript fetch (#843) (#845)

(normalize) treat LRG transcript references as bare for EINTRONIC (#834) (#844)

(project) genomic projection of c.* variants in the 3'UTR poly-A region (NM_003002.2; feat(reference): provision genomic exon structure for corpus-pinned old transcript versions (g.↔c. projection) #790 residual) (#839)

(project) wire rna_description axis and frame predicted r. from input (#838)

(vcf) drop per-sample genotype when splitting multi-allelic records (#841)

(reference) apply cdot CIGAR during transcript synthesis, decline on insertions (#831)

(project) force initiator Met at residue 1 for non-AUG ref-protein translation (#836)

(reference) suppress derived-tx injection for the feat(reference): provision genomic exon structure for corpus-pinned old transcript versions (g.↔c. projection) #790 producer (#835)

(reference) cover canonical-sequence reingestion through the provider (#791) (#832)

(vcf) correct genomic anchor-base recovery and consolidate NC_→chrom mapping (#821)

(vcf) emit RefSeq NC_ accessions on the genomic HGVS axis (#820)

(equivalence/service) make unsupported variant classes explicit (#816)

(data/cdot) drop frequently-wrong NM_→NP_ protein-accession inference (#815)

(vcf) classify coding indels by typed NaEdit and emit Frameshift (#817)

(error) give TranscriptVersionNotExact a distinct error code (E2004) (#814)

(normalize) resolve legacy GENE_v001 selector against the NG_ parent's hosted transcript (#792) (#793)

decline silent transcript version substitution in normalization and projection (#787)

(project) report p.? for an initiation-codon variant on a non-AUG transcript (#772)

(data) anchor minus-strand intronic offsets to the correct exon end (#766)

(convert) map c.*N+offset 3'UTR positions past a transcript terminus (#765)

(normalize) resolve the transcript for a genomic-context c. cross-reference payload (#654) (#756)

(normalize) reject overlapping insertions in cis alleles (fix(validate): reject HGVS-invalid inputs ferro currently accepts (errors axis) #486 EOVERLAP) (#749)

(data) load cdot exons in the HGVS coordinate convention (#748)

(project) re-normalize projected genomic variants in their own frame (#741)

(normalize) normalize r. edits carrying the RNA base u (#736) (#738)

(normalize) extend the exon/intron 3′ rule to n. and r. variants (#704) (#734)

(parser) accept a parenthesized gene-selector in a cross-reference insert (#730)

(reference) forward dropped methods through Arc/Box provider wrappers (#726)

(project) resolve range-reference insertions against the NG_/LRG_ parent before de-anchoring (#708)

(reference) resolve cdot version-exact in normalize, never substitute a sibling version (#717)

(project) re-anchor the genomic axis on the single-transcript projection path (#702) (#703)

(normalize) correct 1-based↔0-based off-by-one in genomic-shuffle fetch (#690)

(normalize) keep W4007 on warn-only intronic-bare resolve-failure (#686)

(project) error instead of emitting invalid HGVS when an NG_/LRG_ re-anchor declines (#655) (#662)

(project) sequence-aware g.↔c. projection across unmodeled exon indels (#644) (#668)

(reference) don't abort LRG mapping scan on a malformed earlier <mapping> (#684)

(check) warn when refseqgene_alignments file is missing (#683)

(python) add missing ErrorType discriminants 41/42 to the type stub (#658)

(normalize) spec-compliant repeat normalization — 3' rotation + flank absorption (#649)

(reference) resolve bare LRG_N genomic accession to its LRG_Ng record (#638)

(benchmark) make setup uta reliable (#623) (#632)

(project) decline protein prediction when the CDS frame is inconsistent (#625) (#628)

(validate) reject intronic offsets on a bare transcript reference (fix(validate): reject HGVS-invalid inputs ferro currently accepts (errors axis) #486 EINTRONIC) (#577)

(project) route stop-disrupting indels to a C-terminal extension (#615) (#621)

(benchmark) time normalize tools by subprocess-internal timer (#609) (#612)

(validate) reject del/dup/delins numeric length not matching the position span (fix(validate): reject HGVS-invalid inputs ferro currently accepts (errors axis) #486 length mismatch) (#565)

(tool-support) assign footnote markers in canonical order (#602)

(reference) report the true secondary-build transcript count (#613)

(normalize) size the intronic shuffle window to the enclosing intron (#573) (#575)

make HashMap-ordered output deterministic (VCF INFO + benchmark reports) (#594)

(parser) bring fast path to full parity with the generic parser (ncRNA, U base, positions, panic) (#560)

(reference) make cdot base→version fallback deterministic (#583)

(conformance) map ECOORDINATESYSTEMMISMATCH to ferro's Parse error (#486) (#579)

(tool-support) address CodeRabbit findings on the matrix generator (#601)

(bench) make the intronic projection fixture self-consistent (#600)

(project) emit nonsense (not fsTer1) for an immediate-stop frameshift (#589)

(project) scan the 3'UTR for a frameshift's new stop (fsTer{K}, not fsTer?) (#587)

(build) repair test code that broke under non-dev feature flags (#580)

(validate) reject delins/del/dup/repeat reference-sequence mismatches in strict mode (#486) (#556)

(validate) reject the RNA base U in a DNA-context edit (fix(validate): reject HGVS-invalid inputs ferro currently accepts (errors axis) #486 ENODNA) (#542)

(normalize) coerce g. on a mitochondrial accession to m. (fix(normalize): canonical edit-form detection (ins→dup, tandem repeat, mito m., allele collapse) #487 mito group) (#541)

(validate) reject c./g./m. on a non-coding RNA reference (fix(validate): reject HGVS-invalid inputs ferro currently accepts (errors axis) #486 coord-system mismatch) (#543)

(normalize) number coding-transcript r. positions CDS-relative (#469) (#539)

(normalize) spec-correct refusal of NG/LRG-parent c. pter/qter flank coordinates (fix(normalize): subtract-with-overflow panics on intronic/pter inputs #488 Phase 2b) (#534)

(project) mid-codon in-frame insertions render as delins, not a clean ins (#511) (#517)

(normalize) guard special/offset genome positions to avoid pterdel overflow panic (#488) (#518)

(reference) decline protein prediction for non-version-exact transcripts (#505) (#519)

(project) extend stop-loss substitution prediction with extTer notation (#498) (#514)

(project) predict p.(Met1?) for CDS-boundary edits reaching the initiation codon (#504) (#513)

(hgvs) distinguish frameshift fsTer? from short fs; predict fsTer? for no-stop frameshifts (#498) (#515)

(project) report p.(Met1?) for initiation-codon variants (#498) (#512)

(project) never emit descending positions in in-frame protein delins (#498) (#510)

(normalize) avoid subtract-overflow panic in minus-strand intronic shuffle (#497)

(test/mutalyzer-normalize) spec-correct bare-NP protein refs (7 cases) (#495)

(reference) flag cdot base-synthesis divergence risk (closes reference: stronger diagnostic for FASTA-vs-cdot reconstruction mismatches (#400 follow-up) #471) (#482)

(error-handling) make detect_swapped_positions axis-aware for m./o. wraparound (closes normalize: make detect_swapped_positions axis-aware so W4001 skips m./o. wraparound ranges (PR #411 follow-up) #467) (#474)

(cdot) plumb transcript protein accession from cdot JSON (#483)

(test/mutalyzer-normalize) accept infos codes ferro does not model (22→11) (#481)

(parser) depth-aware separator scan in expanded allele entrypoints (#476)

(error-handling) extend W3009/W3010 corrector to uncertain-stop forms (#461)

(parser) reject single-position insertion per insertion.md:95-101 (#446) (#450)

(edit) drop brackets on single-payload InsertedSequence::Complex (#443)

(service) extend frameshift classifier span_len to Deletion + Duplication (closes service(effect): extend frameshift classifier span_len to Deletion + Duplication arms (#394 follow-up) #427) ([fix(service): extend frameshift classifier span_len to Deletion + Duplication (closes #427) #435]

coderabbitai · 2026-06-13T22:01:50Z

Walkthrough

Bumps the crate version in Cargo.toml from 0.6.0 to 0.7.0 and adds the corresponding ## [0.7.0] release entry (2026-06-15) to CHANGELOG.md, covering ### Added, ### Fixed, and ### Other sections.

Changes

v0.7.0 Release

Layer / File(s)	Summary
Version bump and 0.7.0 changelog entry `Cargo.toml`, `CHANGELOG.md`	`package.version` incremented to `0.7.0`; `CHANGELOG.md` gains the full release block with Added (features, parsers, protocols, benchmarks), Fixed (normalization, projection, validation, parsing), and Other (CI, tooling, performance, conformance) subsections.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

fulcrumgenomics/ferro-hgvs#2: Same pattern — Cargo.toml version field bump paired with a CHANGELOG.md release entry, no Rust source changes.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title 'chore: release v0.7.0' directly reflects the main change: a version bump from 0.6.0 to 0.7.0 documented in CHANGELOG.md and Cargo.toml.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

✨ Finishing Touches

📝 Generate docstrings

Create stacked PR
Commit on current branch

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch release-plz-2026-06-13T22-01-39Z

_{Comment @coderabbitai help to get the list of available commands.}

nh13 · 2026-06-15T04:26:26Z

@coderabbitai resume

nh13 · 2026-06-15T04:26:27Z

@coderabbitai review

coderabbitai · 2026-06-15T04:26:31Z

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Reviews resumed.

coderabbitai · 2026-06-15T04:26:33Z

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Review finished.

Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.

nh13 · 2026-06-15T08:26:25Z

@coderabbitai resume

nh13 · 2026-06-15T08:26:26Z

@coderabbitai review

coderabbitai · 2026-06-15T08:26:31Z

✅ Action performed

Reviews resumed.

nh13 force-pushed the release-plz-2026-06-13T22-01-39Z branch 8 times, most recently from fce335e to d715467 Compare June 15, 2026 03:10

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nh13 force-pushed the release-plz-2026-06-13T22-01-39Z branch 14 times, most recently from 98c8578 to f0b6eb4 Compare June 16, 2026 22:56

nh13 changed the title ~~chore: release v0.7.0~~ chore: release v0.6.1 Jun 17, 2026

nh13 force-pushed the release-plz-2026-06-13T22-01-39Z branch from f0b6eb4 to 84836f1 Compare June 17, 2026 06:44

nh13 changed the title ~~chore: release v0.6.1~~ chore: release v0.7.0 Jun 17, 2026

nh13 force-pushed the release-plz-2026-06-13T22-01-39Z branch 12 times, most recently from d008b33 to 94b9b94 Compare June 18, 2026 00:03

chore: release v0.7.0

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chore: release v0.7.0#633

chore: release v0.7.0#633
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🤖 New release

⚠ ferro-hgvs breaking changes

0.7.0 - 2026-07-02

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⚠ `ferro-hgvs` breaking changes

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