Fix/819 Fix incorrect g->c mapping when CIGAR alignment gaps overlap variant interval#823
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When a genomic delins spans a position where the CIGAR alignment has an I-segment (genomic bases absent from the transcript), both variant endpoints can land in normal = segments so pos_c.uncertain remains False. The previous code path would strand-flip the edit without adjusting for the missing transcript base, producing an incorrect transcript edit. Fix: add _variant_has_internal_gap() and _gap_segments_within_pos_g() helpers that detect I/D segments strictly inside the variant interval, and route these cases through _get_altered_tx_sequence() which correctly filters genomic-only bases before building the transcript edit. Also refactors _i_segment_offsets_in_pos_g into the new unified _gap_segments_within_pos_g. Tests: update expected value for the adjacent-I-segment case (c.527_532delinsTGTGA, which is the correct result since the I-segment at g.119027727 is outside the variant g.119027721-119027726), and add a new test for the true internal-gap case (g.119027726_119027728delinsTT -> c.526_527delinsAA). Closes: hgvs-cl9, hgvs-hqa, hgvs-83z, hgvs-wma, hgvs-o26 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…internal or spanning alignment gaps.
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Closes #819
Problem
The g_to_c (and g_to_n) mapping in VariantMapper produced incorrect results for two related cases involving CIGAR alignment gaps:
Both cases are manifestations of issue #819 (the "double gap" problem).
Fix
Added helper methods to VariantMapper:
_gap_segments_within_pos_g(mapper, pos_g)— returns all I/D CIGAR segments strictly inside a genomic interval (replaces the earlier _i_segment_offsets_in_pos_g)._variant_has_internal_gap(mapper, var_g)— returns True when a gap segment lies strictly inside the variant interval (both endpoints in = regions)._expand_pos_g_for_adjacent_gap(mapper, var_g)— extends the genomic position to include any I-segment immediately adjacent to the variant boundary.The mapping logic in
g_to_candg_to_nnow checks for these cases before the strand-flip path and routes them through _get_altered_tx_sequence(), which correctly filters out genomic-only bases when reconstructing the transcript edit.Tests
Three new test cases in test_hgvs_assemblymapper.py: