byte index out of bounds for GRCh37:10:5139789:A:AGTG

[holtgrewe]

Describe the bug
When annotating GRCh37:10:5139789:A:AGTG with mehari, hgvs::mapper crashes.

To Reproduce
Steps to reproduce the behavior:

1. Annotate said variant.
2. See the error trace at bottom

Expected behavior
Annotation should work.

Screenshots
N/A

Additional context

thread 'main' panicked at 'byte index 1 is out of bounds of ``', /opt/conda/conda-bld/mehari_1695048327300/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hgvs-0.11.0/src/mapper/altseq.rs:701:56
stack backtrace:
   0: rust_begin_unwind
             at /rustc/5680fa18feaa87f3ff04063800aec256c3d4b4be/library/std/src/panicking.rs:593:5
   1: core::panicking::panic_fmt
             at /rustc/5680fa18feaa87f3ff04063800aec256c3d4b4be/library/core/src/panicking.rs:67:14
   2: core::str::slice_error_fail_rt
   3: core::str::slice_error_fail
             at /rustc/5680fa18feaa87f3ff04063800aec256c3d4b4be/library/core/src/str/mod.rs:87:9
   4: hgvs::mapper::altseq::AltSeqToHgvsp::build_hgvsp
   5: hgvs::mapper::variant::Mapper::c_to_p::{{closure}}
   6: alloc::vec::in_place_collect::<impl alloc::vec::spec_from_iter::SpecFromIter<T,I> for alloc::vec::Vec<T>>::from_iter
   7: core::iter::adapters::try_process
   8: hgvs::mapper::variant::Mapper::c_to_p
   9: hgvs::mapper::assembly::Mapper::c_to_p
  10: mehari::annotate::seqvars::csq::ConsequencePredictor::build_ann_field
  11: <core::iter::adapters::map::Map<I,F> as core::iter::traits::iterator::Iterator>::try_fold
  12: alloc::vec::in_place_collect::<impl alloc::vec::spec_from_iter::SpecFromIter<T,I> for alloc::vec::Vec<T>>::from_iter
  13: core::iter::adapters::try_process
  14: mehari::annotate::seqvars::csq::ConsequencePredictor::predict
  15: mehari::annotate::seqvars::run_with_writer
  16: mehari::annotate::seqvars::run
  17: tracing_core::dispatcher::with_default
  18: mehari::main
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

This happens when calling c_to_p on the following variant:

NM_001253909.2:c.416_417insGTG

CdsVariant {
    accession: Accession {
        value: "NM_001253909.2",
    },
    gene_symbol: None,
    loc_edit: CdsLocEdit {
        loc: Certain(
            CdsInterval {
                start: CdsPos {
                    base: 416,
                    offset: None,
                    cds_from: Start,
                },
                end: CdsPos {
                    base: 417,
                    offset: None,
                    cds_from: Start,
                },
            },
        ),
        edit: Certain(
            Ins {
                alternative: "GTG",
            },
        ),
    },
}

[holtgrewe]

Hm, variantvalidator.org does not like this:

[holtgrewe]

I assume that we have to run the projection through the original hgvs Python code and see what happens there.

[holtgrewe]

The VEP prediction is correct * => ** plus inframe_insertion&stop_retained_variant.

#Uploaded_variation	Location	Allele	Consequence	IMPACT	SYMBOL	Gene	Feature_type	Feature	BIOTYPE	EXON	INTRON	HGVSc	HGVSp	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	DISTANCE	STRAND	FLAGS	SYMBOL_SOURCE	HGNC_ID	MANE_SELECT	MANE_PLUS_CLINICAL	TSL	APPRIS	REFSEQ_MATCH	REFSEQ_OFFSET	GIVEN_REF	USED_REF	BAM_EDIT	SIFT	PolyPhen	AF	CLIN_SIG	SOMATIC	PHENO	PUBMED	MOTIF_NAME	MOTIF_POS	HIGH_INF_POS	MOTIF_SCORE_CHANGE	TRANSCRIPTION_FACTORS
.	10:5139789-5139789	GTG	inframe_insertion,stop_retained_variant	MODERATE	AKR1C3	8644	Transcript	NM_001253909.2	protein_coding	3/3	-	-	-	447-448	416-417	139	/*	taa/taGTGa	-	-	1	-	EntrezGene	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-