Norm replacing reference base should be included in old-rec-tag

[davmlaw]

Thanks for all your hard work making a great tool!

While processing a normalized VCF I want to see if the reference base was replaced

I think if norm changes the variant via replacing reference base it should write out the --old-rec-tag - this seems to fit with the help "Annotate modified records with INFO/STR indicating the original variant"

Example, running --check-ref=s --old-rec-tag=BCFTOOLS_OLD_VARIANT

NC_000004.12	51382327	14565929	N	<DEL>	.	.	SVLEN=-2000;SVTYPE=DEL;END=51384327
NC_000004.12	89258449	14565930	N	<DUP>	.	.	SVLEN=20474;SVTYPE=DUP;END=89278923

Output:

NC_000004.12	51382326	14565929	a	<DEL>	.	.	SVLEN=-2000;SVTYPE=DEL;END=51384326;BCFTOOLS_OLD_VARIANT=NC_000004.12|51382327|c|<DEL>
NC_000004.12	89258449	14565930	t	<DUP>	.	.	SVLEN=20474;SVTYPE=DUP;END=89278923

problems:
1st record should be NC_000004.12|51382327|N|<DEL> showing old record but is NC_000004.12|51382327|c|<DEL> (POST ref replace)
2nd record should have INFO field record was modified

[davmlaw]

If someone agrees this is the right solution I'm happy to make a pull request

[pd3]

This is now done, please try it out. Thank you for the issue.