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bcftools merge -m none hangs forever (while allocating more and more memory) #1164

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freeseek opened this issue Feb 25, 2020 · 2 comments
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bcftools merge -m none hangs forever (while allocating more and more memory) #1164

freeseek opened this issue Feb 25, 2020 · 2 comments

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@freeseek
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The following code reproduces the issue:

(echo ">chr1"; \
echo "ACGT") > ref.fa

(echo "##fileformat=VCFv4.2"; \
echo "##contig=<ID=chr1,length=248956422>"; \
echo "##INFO=<ID=END,Number=1,Type=Integer,Description=\"Stop position of the interval\">"; \
echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"; \
echo -e "chr1\t1\t.\tA\t<NON_REF>\t.\t.\tEND=2") | \
  bcftools view -Oz -o a.vcf.gz && bcftools index -ft a.vcf.gz

(echo "##fileformat=VCFv4.2"; \
echo "##contig=<ID=chr1,length=248956422>"; \
echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"; \
echo -e "chr1\t1\t.\tA\tC\t.\t.\t.") | \
  bcftools view -Oz -o b.vcf.gz && bcftools index -ft b.vcf.gz

bcftools merge -g ref.fa a.vcf.gz b.vcf.gz -m none -o /dev/null
@pd3 pd3 closed this as completed in 2de40a8 Mar 5, 2020
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pd3 commented Mar 5, 2020

Thanks for the bug report, this is now fixed. If you spot anything odd, please let me know.

pd3 added a commit that referenced this issue Apr 4, 2023
@pd3
Revamped line matching code to fix problems in gVCF merging
60c65eb 
Previously gVCF blocks were correctly split but in some cases FORMAT
fields would not be updated at split sites.

This commit revamps the line matching code, adds comments and makes it
more understandable.

Fixes #1891 and revisits #1164
@pd3
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pd3 commented Apr 4, 2023

It turns out the problem was fixed only partially, gVCF blocks wouldn't fill in FORMAT fields at split positions, see a related problem here #1891, now fixed.

pd3 added a commit that referenced this issue Apr 18, 2023
@pd3
More fixes in gVCF merging
2f482de 
Genotypes at the ends of gVCF blocks were in some cases still unfilled, even after
the 60c65eb fix.

Fixes #1910, see also #1891 and #1164.
@pd3 pd3 mentioned this issue Apr 18, 2023
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@pd3 @freeseek