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Fix on-the-fly indexing of VCF w.r.t virtual offsets. #1837

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Sep 12, 2024
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Fix on-the-fly indexing of VCF w.r.t virtual offsets. #1837

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4 changes: 4 additions & 0 deletions NEWS
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,10 @@ Bug fixes
* Fix small OSS-Fuzz reported issues with CRAM encoding and long
CIGARS and/or illegal positions. (PR #1775, PR #1801, PR #1817)

* Fix issues with on-the-fly indexing of VCF/BCF (bcftools --write-index)
when not using multiple threads. (PR #1837. Fixes samtools/bcftools#2267,
reported by Giulio Genovese)

* Stricter limits on POS / MPOS / TLEN in sam_parse1(). This fixes
a signed overflow reported by OSS-Fuzz and should help prevent other
as-yet undetected bugs. (PR #1812)
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2 changes: 2 additions & 0 deletions vcf.c
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Expand Up @@ -4238,6 +4238,8 @@ int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
if ( fp->format.compression!=no_compression ) {
if (bgzf_flush_try(fp->fp.bgzf, fp->line.l) < 0)
return -1;
if (fp->idx && !fp->fp.bgzf->mt)
hts_idx_amend_last(fp->idx, bgzf_tell(fp->fp.bgzf));
ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l);
} else {
ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
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