Fix 10 assorted medium-severity bugs across multiple files#2537
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix 10 assorted medium-severity bugs across multiple files#2537sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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- vcffilter.c: Change max_qual from int to float to avoid truncation of
fractional QUAL values
- vcfview.c: Guard args->ac[1] access with n_allele>=2 check for
ALLELE_ALT1 filtering to prevent out-of-bounds on REF-only sites
- convert.c: Invert bcf_gt_is_phased() condition in process_gt_to_hap
and process_gt_to_hap2 ('*' marks unphased, not phased)
- convert.c: Use gt_id instead of fmt->id for GT header existence check
in process_pbinom
- convert.c: Fix off-by-one in allele bounds check (al >= n_allele,
not al > n_allele) since allele index is 0-based
- dist.c: Fix double-counting in dist_insert_n; dist_insert already
increments nvalues by 1, so add cnt-1 not cnt
- bin.c: Prevent bin_get_idx from returning -1 when value is below
first bin boundary
- read_consensus.c: Fix loop condition from j<dfreq[i].len[j] to
dfreq[i].len[j] (nonzero check) matching the pattern used elsewhere
- gff.c: Fix Mt_rRNA returning GF_MT_tRNA instead of GF_MT_rRNA
(copy-paste error)
- gff.c: Fix strncmp length for "lncRNA" from 7 to 6
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Summary
max_qualint→float (QUAL truncation in IndelGap filtering)ac[1]access withn_allele >= 2for 4 ALLELE_ALT1 pathsbcf_gt_is_phasedfor unphased*marker in hap output (2 functions)gt_idinstead offmt->idin GT existence checkal > n_alleletoal >= n_allelenvaluesoff-by-one indist_insert_n(counted cnt+1 instead of cnt)bin_get_idxreturning -1 for values below first binj<dfreq[i].len[j]todfreq[i].len[j](nonzero check)Mt_rRNAreturningGF_MT_tRNA(copy-paste error)strncmp("lncRNA", 7)to length 6 — was never matching lncRNA biotypeFixes #2496
Test plan