bcftools reheader -f/--fai does not preserve the order of the contigs (even when it could)

Start by reproducing the issue with the provided ref.fai, chr1.bcf, and chr2.bcf commands, then compare the outputs of bcftools reheader and concat -n. Trace the reheader and concat command entry points to determine how contig order is handled. Done means files reheadered from the same index can be concatenated with -n without --naive-force and without changing record interpretation.

I have noticed the following behavior.

Suppose I have two files and a reference index:

echo -e "##fileformat=VCFv4.2\n##contig=<ID=chr1,length=248956422>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr1\t1\t.\tA\tC\t.\t.\t." | bcftools view --no-version -Ob -o chr1.bcf
echo -e "##fileformat=VCFv4.2\n##contig=<ID=chr2,length=242193529>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr2\t1\t.\tG\tT\t.\t.\t." | bcftools view --no-version -Ob -o chr2.bcf
echo -e "chr1\t248956422\t112\t70\t71\nchr2\t242193529\t252513167\t70\t71" > ref.fai

I then use the reference index to reheader the VCFs:

bcftools reheader -f ref.fai -o chr1.reheader.bcf chr1.bcf
bcftools reheader -f ref.fai -o chr2.reheader.bcf chr2.bcf

Unintuitively, the order of the contigs is not the same in the two files now:

$ bcftools view --no-version chr1.reheader.bcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	1	.	A	C	.	.	.

$ bcftools view --no-version chr2.reheader.bcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr1,length=248956422>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr2	1	.	G	T	.	.	.

This makes it impossible to concatenate files with the -n option:

$ bcftools concat -n chr1.reheader.bcf chr2.reheader.bcf
Checking the headers of 2 files.
Cannot use --naive, use --naive-force instead: different order the tag contig/chr1 in chr1.reheader.bcf vs chr2.reheader.bcf

And, of course, using the --naive-force option would cause inappropriate behavior:

$ bcftools concat -n --naive-force chr1.reheader.bcf chr2.reheader.bcf | bcftools view --no-version
Concatenating chr1.reheader.bcf	0.000709 seconds
Concatenating chr2.reheader.bcf	0.000503 seconds
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	1	.	A	C	.	.	.
chr1	1	.	G	T	.	.	.

However, I do understand why bcftools reheader -f would not want to reorder the contigs, as that would potentially cause the VCF file to become unsorted. At the same time I thought that the bcftools concat -n option was exactly supposed to work after the header of the VCF files were updated with the bcftools reheader -f option.