Fix csq consequence prediction: sref offset, OOB codon, stop codon, splice#2527
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Fix csq consequence prediction: sref offset, OOB codon, stop codon, splice#2527sirus20x6 wants to merge 3 commits intosamtools:developfrom
sirus20x6 wants to merge 3 commits intosamtools:developfrom
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When a reverse-strand compound variant has ibeg forced to HAP_SSS (due to frameshift + start_lost), csq->pos was set from ref_node (=iend) but csq_push was called with ibeg's record. Since they are at different genomic positions, the vbuf lookup at iend's position could not find ibeg's record, triggering: "This should not happen.. <chr>:<pos> <variant>" Fix by setting csq->pos to ibeg's position in the SSS branch so the position and record are consistent for the vbuf lookup.
1. tscript_splice_ref: Fix trailing pad copy offset to start after the last CDS exon (was incorrectly copying from the beginning of it). 2. dna2aa/cdna2aa/dna2stop/cdna2stop macros: Guard against out-of-bounds access when non-ACGT bases (e.g. 'N') produce codon indices > 63. Return 'X' (unknown amino acid) or 0 (not a stop) instead. 3. hap_add_csq and test_cds_local: After searching tseq_stop for '*', compare the found index against tseq_stop.l (not tseq.l), matching the string that was actually iterated. 4. test_splice: Use loop variable rec->d.allele[i] instead of hardcoded rec->d.allele[1] when checking for symbolic/missing alleles.
This was referenced Mar 26, 2026
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Summary
tseq.linstead oftseq_stop.l(2 occurrences)test_splicechecking hardcodedallele[1]instead of loop variableallele[i]Fixes #2478. Relates to #2393.
Test plan