# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
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test_that('check tabix', {
	if (check.binary('tabix', verbose = TRUE)) {
		vcf <- testthat::test_path('data/CosmicCodingMuts_v66_20130725_ex.vcf.gz');
		regions <- get.example.regions();
		regions$a <- bedr.sort.region(regions$a);

		a.nochr <- gsub('^chr', '', regions$a);

		b <- c('chr1:10-100000','chr10:100-100000');
		b.nochr <- c('1:10-100000','10:100-100000');

		b.nochr.matrix <- index2bed(b.nochr);

		# bad region
		expect_error(tabix('meow', vcf, verbose = TRUE));

		# no chr
		expect_error(tabix(a.nochr, vcf, verbose = TRUE));

		# missing file
		expect_error(tabix(a.nochr, 'meow', check.chr = FALSE, verbose = TRUE));

		# check the length of output
		expect_equal(nrow(tabix(a.nochr, vcf, verbose = T, check.chr = FALSE)), NULL);
		expect_equal(nrow(tabix(b.nochr, vcf, verbose = T, check.chr = FALSE)), 6);
	
		# check the header is included
		expect_equal(colnames(tabix(b.nochr, vcf, verbose = T, check.chr = FALSE)), c('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO')); 

		# check header is correct length
		expect_equal(length(attributes(tabix(b.nochr, vcf, verbose = T, check.chr = FALSE))$header), 13);
		}
	})