remove redundant vcf format conversion function

Author: alkaZeltser

tests/testthat/helper-test-utils.R

@@ -1,37 +1,3 @@
-# function that converts test data in long format into wide format
-
-convert.long.vcf.to.wide.vcf <- function(long.vcf) {
-    long.vcf <- as.data.frame(long.vcf);
-    fixed.colnames <- c('CHROM', 'POS', 'ID', 'REF', 'ALT');
-    fixed.data <- long.vcf[, fixed.colnames];
-    fixed.data$variant.id <- paste0(fixed.data$CHROM, ':', fixed.data$POS);
-    fixed.data <- unique(fixed.data); # remove duplicates
-    # convert to data.table
-    fixed.data <- data.table::as.data.table(fixed.data);
-    #fixed.data$allele.matrix.row.index <- seq_len(nrow(fixed.data));
-
-    variant.id <- paste0(long.vcf$CHROM, ':', long.vcf$POS);
-    allele.matrix <- as.matrix(get.variant.by.sample.matrix(
-        long.data = long.vcf,
-        row.id.cols = c('CHROM', 'POS'),
-        value.col = 'gt_GT_alleles'
-        ));
-
-    # sort allele matrix in order of corresponding fixed data variant id
-    allele.matrix <- allele.matrix[match(fixed.data$variant.id, rownames(allele.matrix)), ];
-
-    # save allele matrix row indices in fixed data
-    fixed.data$allele.matrix.row.index <- seq_len(nrow(allele.matrix));
-
-    # format output according to import.vcf standards
-    output <- list(
-        genotyped.alleles = allele.matrix,
-        vcf.fixed.fields = fixed.data
-        );
-
-    return(output);
-
-    }
 
 initialize.defaults <- function() {
     phenotype.data <- NULL