R/is.sorted.region.R

In uclahs-cds/public-R-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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is.sorted.region <- function(x, method = "lex", engine = "unix", check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.merge = TRUE, verbose = FALSE) {

	x.sort    <- bedr.sort.region(x, method = method, engine = engine, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.merge = check.merge, verbose = FALSE);
	is.sorted <- all(x == x.sort); # use data.frame to drop attributes

	catv(" * Checking sort order... ")
	if (is.sorted) {
		catv("PASS\n");
		}
	else {
		catv("FAIL\n")
		catv(paste0("   The input for object is not *lexographically* ordered!\n   This can cause unexpected results for some set operations.\n   try: x <- bedr.sort.region(x)\n"));
		}
		
	
	return(is.sorted);
	}