## this is the R script:
## called from the matching .sh script (which passes in the parameters)


# getting file name as passed from the bash script
passed_args<-commandArgs(trailingOnly = TRUE)

# limits the snp reference file to only the chrom of interest
chr_num<-passed_args[3]

# variable for the snp151 reference file - expecting at least a CHROM, POS, and rsid columns in the snp ref file
snp_file<-passed_args[4]

# imports the reference data file for the SNPs (old vcf "ID" column contains snp_22_30192384; new "ID" should be the rsid)
snp_ref<-read.delim(snp_file, header=TRUE, sep=" ")
snp_ref<-snp_ref[which(snp_ref$CHROM==chr_num),]
snp_ref$variant_id<-paste("snp_",snp_ref$CHROM, "_",  snp_ref$POS, sep="")
snp_ref$CHROM<-as.integer(snp_ref$CHROM)
paste("Chr ", chr_num, "SNPs found: ", nrow(snp_ref), sep="")

#get from args[] the .vcf file
vcf_file_name<- passed_args[1]

#find the first line of actual data
header_rows_skip<-as.integer(passed_args[2])-1

#imports the file into a table without the metadata lines
body_only_VCF<-read.delim(vcf_file_name, header = TRUE, skip=header_rows_skip, sep="\t")
colnames(body_only_VCF)[1]<-"CHROM"
paste("orig VCF file rows ", nrow(body_only_VCF))

#removes anything where the reference or alternate allele is not G/C/T/A (i.e. narrows down vcf working file to just SNPs)
body_only_VCF<-body_only_VCF[which(body_only_VCF$REF %in% c("A","T","C","G") & body_only_VCF$ALT %in% c("A","T","C","G")),]
paste("VCF filtered to only SNPS ", nrow(body_only_VCF))

#merges the VCF file with records that have a matching lookup in the snp_ref table
final_VCF<-merge(body_only_VCF,snp_ref, all = FALSE )
paste("Merge complete - matched VCF records by CHROM and POS", nrow(final_VCF))

#get final file column order
VCF_col_names<-names(body_only_VCF)

#trying to free up some memory
rm(body_only_VCF)

#udpated the ID column and removes the columns from snp_ref
final_VCF$ID<-final_VCF$rsid
final_VCF<-final_VCF[,VCF_col_names]

#rename first col to #CHROM to match vcf file formatting
colnames(final_VCF)[1]<-"#CHROM"

#write final file to the vcf_directory
final_file=paste(substr(vcf_file_name, 1, nchar(vcf_file_name)-4), "_updated2.vcf", sep="")
write.table(final_VCF, file = final_file, sep="\t", row.names = FALSE, quote=FALSE)