public class Bref
extends java.lang.Object
Class Bref
has methods for reading and writing phased,
non-missing genotypes that are stored in a "bref" binary VCF file.
Instances of class Bref
are not thread-safe.
Modifier and Type | Field and Description |
---|---|
static int |
EOF
The end of file character for a bref file.
|
static int |
INITIAL_NUMBER
The initial long in a bref file created with this bref version.
|
Modifier and Type | Method and Description |
---|---|
static java.lang.String[] |
alleleString(int permIndex,
int length)
Returns an array that is obtained by taking the first
length
elements of the specified permutation of "A", "C", "G", and "T". |
static void |
main(java.lang.String[] args)
The
main() method is the entry point to the bref program. |
public static final int INITIAL_NUMBER
public static final int EOF
public static void main(java.lang.String[] args)
main()
method is the entry point to the bref program.
See the usage() method for usage instructions.args
- the command line argumentspublic static java.lang.String[] alleleString(int permIndex, int length)
length
elements of the specified permutation of "A", "C", "G", and "T".
The list of 24 permutations of "A", "C", "G", and "T" are sorted
in lexicographic order.permIndex
- an index of a permutation of the bases "A",
"C", "G", and "T"length
- the number of elements in the returned arraylength
elements of the specified permutation of "A", "C", "G", and "T"java.lang.IndexOutOfBoundsException
- if
permIndex < 0 || permIndex >= 24
java.lang.IndexOutOfBoundsException
- if length < 0 || length >= 4