fn parse_bed_file (input: &str) -> HashMap<String,Vec<u64>>{
	assert!(
		Path::new(input).exists(),
		"ERROR: BED file {} does not exist!",
		input,
	);
	let mut bed_result : HashMap<String,Vec<u64>> = HashMap::new();
	let mut bed = bio::io::bed::Reader::from_file(input).unwrap();
	for entry in bed.records(){
		let record = entry.expect("ERROR: wrong BED record");
		if record.end()-record.start()>1 {
			panic!("ERROR: entry {:?} contained not a position but a range!",&record);
		}
		bed_result
			.entry(record.chrom().to_string())
			.or_insert_with(Vec::new)
			.push(record.start());
	
	};
	for (_, entries) in bed_result.iter_mut(){
		entries.sort_unstable();
		entries.dedup();
	}
	bed_result
}
// this simply takes a BED file and organizes entries in a Hashmap
// where they are organized by chromosome which should speedup
// later the indexed access
this simply takes a BED file and organizes entries in a Hashmap
where they are organized by chromosome which should speedup
later the indexed access
this simply takes a BED file and organizes entries in a Hashmap where they are organized by chromosome which should speedup later the indexed access
fn parse_bed_file (input: &str) -> HashMap<String,Vec<u64>>{
	assert!(
		Path::new(input).exists(),
		"ERROR: BED file {} does not exist!",
		input,
	);
	let mut bed_result : HashMap<String,Vec<u64>> = HashMap::new();
	let mut bed = bio::io::bed::Reader::from_file(input).unwrap();
	for entry in bed.records(){
		let record = entry.expect("ERROR: wrong BED record");
		if record.end()-record.start()>1 {
			panic!("ERROR: entry {:?} contained not a position but a range!",&record);
		}
		bed_result
			.entry(record.chrom().to_string())
			.or_insert_with(Vec::new)
			.push(record.start());
	};
	for (_, entries) in bed_result.iter_mut(){
		entries.sort_unstable();
		entries.dedup();
	}
	bed_result
}
fn parse_bed_file ( input : & str ) -> HashMap < String , Vec < u64 > > { assert ! ( Path new ( input ) exists ( ) " " input ) ; let mut bed_result : HashMap < String , Vec < u64 > > = HashMap :: new ( ) ; let mut bed = bio :: io :: bed :: Reader :: from_file ( input ) . unwrap ( ) ; for entry in bed . records ( ) { let record = entry . expect ( " " ) ; if record . end ( ) - record . start ( ) > 1 { panic ! ( " " record ) ; } bed_result . entry ( record . chrom ( ) . to_string ( ) ) . or_insert_with ( Vec :: new ) . push ( record . start ( ) ) ; } ; for ( _ , entries ) in bed_result . iter_mut ( ) { entries . sort_unstable ( ) ; entries . dedup ( ) ; } bed_result }
this simply takes a BED file and organizes entries in a Hashmap
where they are organized by chromosome which should speedup
later the indexed access
this simply takes a BED file and organizes entries in a Hashmap where they are organized by chromosome which should speedup later the indexed access
input
&str
input
&str