Running bcftools consensus with -c flag causes segmentation error with specific variants

[rahulg603]

A segmentation fault is produced with the following command:

bcftools consensus -f fasta_subset.fasta -o sequence_applied.fasta -c /out.chain input_vcf.gz

when the .fasta file contains subsets of the genome and the VCF file contains a deletion which spans the edge of the genome subset. A reproducible example can be seen with the following fasta:

>chrX:70125625-70126807
CTTGGGTTCAAGCGATTTTGCTGTCTCAGCCTCCCAAGTAGCTGTGATTACAGGCGAGTGCCACCACGCCCAGCTGATTT
TTTGTATTTTTAGTAGAGGTGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGGCCTCAAGTGATCTGCCCAC
GTCAGCCTCCCAGAGTGCTGAGATTACAGGTGTGAGCCACTGCGCCTGGCCTGAGTTATTTTTGTTGATGACAGCTAAGG
TTGTAAAGCAAGGCTGTCCTAGCAGTGTGAAGAAAATAACTCGGGTACTGTATACAGCCTTTAGGGAGGTGGTGATGAGT
GTAATTAAGAGGGCTCAGCCATTGGTATATGATGTGCTTGTGGTTTCAATGATGAGATCGTTGGAGTAGAAGCCTGTAAG
GCATGGTATACCTGCGAGGCTGCCAATGATAAGTGAGGAGGAAGTGAAGATGTCTTGTTCATTATTTAGATTATGAATAA
TAGATCCAGAGCATATACACTATGGCTTTAAGAAAGTGTGAGTATAGATATGAAGAAATGCTAGGTGAAGTTGATTAATG
CCAGTTGTAACTACTGAGACCTAGTTGACTCGAGGTAGAAAATGCTACAATTTTTTTGATATCATTTTGTGTTAGAGCTC
AGATCGCTGTGAATAAAGTGGTGATGGCACCTAAGCATAGTGTAAGTGCCTGAATGATTATATTATTTTGTATTAAGGGG
TAAAAGCAAATTAGTAGGCAGATACCTGCTACTACTATTATGCTAGAATGAAGGAGGGCAGAGATGGAAGTTGGGCCTTC
CATGGCTGATGGAAGTCATGGATGAAGTCCAAATGGAACTGATTTGCCAGTTGCTGCTACTAGGAGCCCAATTAGTAGGA
GGATATTGGGGTTGGGGTTAAGAATAAATATCTGTTGAAATTCTCATGTATTAGAGAATGATAGGAACCATGCTATTGCT
AAGATGAAGCCAATGTCTCCAATGCGATTATGTAGAATTGCTTATAGGGCTGCTGTGTTAGCATCTGTTCAGCCACATCA
TCAGCTGATTAGTAGTAAAGATACGATACCTGCTCCCTCTCATCCAATGAAAAGTTGGTAGTGACTAGAATTAGTATGGT
GATGAGAAATGTGAGTAAATATTTGAAGAATGATTGATATTAGGGCCTGAGTGTATATATAAT
>chrX:70126914-70126916
CCT

and the following VCF:

##fileformat=VCFv4.2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test
chrX	70126806	.	ATATT	A	.	PASS		GT	1/1

Notably no issue occurs if -c is not specified. I believe this error also only crops up when there are multiple intervals; if I modify the above .fasta to just have the first interval the command runs without issue.

Here is the current version:

bcftools 1.14
Using htslib 1.14
Copyright (C) 2021 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

[pd3]

This should be now fixed by fe0ba97, please try it out

[rahulg603]

Brilliant, this looks like it works like a charm! Thanks.