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@pd3 Thanks, that's the feeling I got when I ran it through valgrind. I honestly wasn't sure whether it made more sense to make the issue here or with htslib, since I imagine it's harder to reproduce on that repo.
pd3
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Oct 3, 2024
When an empty VCF file with a header but no data lines is indexed,
tbx_seqnames() called via bcf_sr_add_reader() returns an empty list.
Consequently, when bcf_sr_regions_next() is called and no in-memory
regions are available, it attempts to read from a file which is
not initialized.
This fixessamtools/bcftools#2286
It seems that
bcftools concat
will segfault if the files it's combining have only headers:I'll attach a header-only VCF file that can be easily used for testing (just copy it to bar.vcf.gz)
foo.vcf.gz
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