write-index does not appear to work from concat command

[ASLeonard]

I was concatting 29 uncompressed vcfs and indexing the output

bcftools concat -o autosomes.vcf.gz --write-index {1..29}.vcf

However, the resultant index is more or less empty, and running bcftools index -n autosomes.vcf.gz returns 0.
Deleting that index and re-indexing (either via tabix -p vcf or bcftools index) produces a larger index that returns the correct number of variants from the previous command.

This seems to also occur if the input to concat is compressed, or with --write-index=tbi, so seems to be general issue rather than a specific combination of events.

This is with

bcftools 1.20-45-g5e7ea8a0-dirty
Using htslib 1.20-54-gfbe5ff6c-dirty

Best,
Alex

[whitwham]

I see what it is doing. In this case it is writing out the VCF in the simplest way (vcf_write_line) which is good for speed but does not contain any index writing code. So all that is produced is the index header with no actual index.

I will look at making it work.