public class GenomicIndexUtil extends Object
Modifier and Type | Field | Description |
---|---|---|
static int |
BIN_GENOMIC_SPAN |
Reports the total amount of genomic data that any bin can index.
|
static int[] |
LEVEL_STARTS |
What is the starting bin for each level?
|
static int |
MAX_BINS |
Reports the maximum number of bins that can appear in a binning index.
|
static int |
MAX_LINEAR_INDEX_SIZE |
|
static int |
UNSET_GENOMIC_LOCATION |
E.g.
|
Constructor | Description |
---|---|
GenomicIndexUtil() |
Modifier and Type | Method | Description |
---|---|---|
static int |
regionToBin(int beg,
int end) |
calculate the bin given an alignment in [beg,end)
Described in "The Human Genome Browser at UCSC.
|
static BitSet |
regionToBins(int startPos,
int endPos) |
Get candidate bins for the specified region
|
public static final int BIN_GENOMIC_SPAN
public static final int[] LEVEL_STARTS
public static final int MAX_BINS
public static final int MAX_LINEAR_INDEX_SIZE
public static final int UNSET_GENOMIC_LOCATION
public static int regionToBin(int beg, int end)
beg
- 0-based start of read (inclusive)end
- 0-based end of read (exclusive)public static BitSet regionToBins(int startPos, int endPos)
startPos
- 1-based start of target region, inclusive.endPos
- 1-based end of target region, inclusive.