0 coordinate overflows in VCF format

[Rapsssito]

As stated here: samtools/bcftools#1753. There is an overflow issue when treating a VCF file with zero positions. Here is an example:

Unsorted VCF

MT	0	1915430843:1	N	]MT:16640]N	99	PASS	.
MT	0	3110098432:1	N	]MT:16638]N	99	PASS	.
MT	16638	3110098432:2	G	G[MT:0[	99	PASS	.
MT	16640	1915430843:2	G	G[MT:0[	99	PASS	.

Commands

bcftools sort test.vcf -o test.sorted.vcf

Sorted VCF

MT	4294967296	3110098432:1	N	]MT:16638]N	99	PASS	.
MT	4294967296	1915430843:1	N	]MT:16640]N	99	PASS	.
MT	16638	3110098432:2	G	G[MT:0[	99	PASS	.
MT	16640	1915430843:2	G	G[MT:0[	99	PASS	.

Note how the 0 from 3110098432:1 has been wrongly changed to 4294967296.

As described by @pd3 in samtools/bcftools#1753 (comment):

This problem is not specific to bcftools sort but to a round trip through BCF via htslib. The format stores 0-based position in hts_pos_t type and 0 coordinate overflows. This needs to be fixed in htslib.

@daviesrob, could you check this out?

[daviesrob]

Fixed by #1476