tests/testthat/test-vcf2bedpe.R

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
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test_that('check_vcf2bedpe', {
  	for (sv.caller in c('gridss', 'delly', 'manta')) {
		vcf.file <- testthat::test_path(paste0('data/', sv.caller, 'SV.vcf.gz'));
  		vcf <- read.vcf(vcf.file, split.info = TRUE);
  		bedpe <- vcf2bedpe(vcf);
  
  		# check bedpe is not empty
  		expect_equal((nrow(bedpe) > 0), TRUE);
  
  		# check the header is included
  		expect_equal(colnames(bedpe), c('CHROM_A', 'START_A', 'END_A', 'CHROM_B', 'START_B', 'END_B', 'ID', 'QUAL', 'STRAND_A', 'STRAND_B', 'SVTYPE')); 
  
  		# if SVTYPE == BND, must have MATEID
  		if (sv.caller == 'gridss') {
  			vcf$vcf <- subset(vcf$vcf, select = -MATEID);
  			expect_error(vcf2bedpe(vcf));
  		}
    	# expect error if vcf is unpacked 
    	expect_error(vcf2bedpe(vcf$vcf));
    
    	# expect error if VCF doesnt have SVTYPE column
    	vcf$vcf <- subset(vcf$vcf, select = -SVTYPE);
    	expect_error(vcf2bedpe(vcf));	
    	}
    })