public class GenomicIndexUtil
extends java.lang.Object
Modifier and Type | Field and Description |
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static int |
BIN_GENOMIC_SPAN
Reports the total amount of genomic data that any bin can index.
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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 and Description |
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GenomicIndexUtil() |
Modifier and Type | Method and Description |
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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 java.util.BitSet |
regionToBins(int startPos,
int endPos)
Get candidate bins for the specified region
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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 java.util.BitSet regionToBins(int startPos, int endPos)
startPos
- 1-based start of target region, inclusive.endPos
- 1-based end of target region, inclusive.