Feature request: norm --remove-duplicates report removed dupes in summary stats

[davmlaw]

Norm produces summary stats, eg:

Lines   total/split/joined/realigned/skipped:	2/0/0/0/0

It would be nice if this included "removed duplicates" (or rmdup or whatever)

Eg sample file w/dupes:

##fileformat=VCFv4.0
##contig=<ID=1,length=249250621,assembly=hg19>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	99167215	rs5776431	CA	C	4675.23	PASS	.
1	99167215	rs5776431	CA	C	4675.23	PASS	.

bcftools norm -f /data/annotation/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --remove-duplicates dupes.vcf

Output:

Lines   total/split/joined/realigned/skipped:	2/0/0/0/0

Suggested output:

Lines   total/split/joined/realigned/skipped/removed_dupes:	2/0/0/0/0/1

[pd3]

I added this to the stats.