fix: avoid adding duplicate CSQ/ANN fields via --retain-ann

[dlaehnemann]

We have cases where we want to ensure that certain ANN columns are in the MAF file, and we generate that list programmatically in a workflow. Currently, this leads to a duplication of any field requested via --retain-ann, that is already in the default list at:

vcf2maf/vcf2maf.pl

Lines 545 to 552 in 0d3f514

	my @ann_cols = qw( Allele Gene Feature Feature_type Consequence cDNA_position CDS_position
	Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL
	SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen
	EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC
	PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL
	HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomADe_AF gnomADe_AFR_AF
	gnomADe_AMR_AF gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF
	);

So this solutions filters out any --retain-add-specified fields that are already in @ann_cols and avoids pushing them onto the column array.

I just looked up all the syntax and tried it in some online perl compiler. So feel free to adjust it to whichever style you might prefer. And obviously to fix any mistakes I might have made.

[dlaehnemann]

I can't directly ask for a review via the interface, so I'll try by pinging in @ckandoth, who seems to have been the main maintainer.

[ckandoth]

Thanks for the PR, and sorry for the delay. Will review and merge shortly.