htsjdk.samtools

Class GenomicIndexUtil

java.lang.Object

htsjdk.samtools.GenomicIndexUtil

public class GenomicIndexUtil
extends java.lang.Object

Constants and methods used by BAM and Tribble indices

Field Summary

Fields

Modifier and Type	Field and 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 Summary

Constructors

Constructor and Description
GenomicIndexUtil()

Method Summary

Modifier and Type	Method and 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 java.util.BitSet	regionToBins(int startPos, int endPos) Get candidate bins for the specified region

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BIN_GENOMIC_SPAN

public static final int BIN_GENOMIC_SPAN

Reports the total amount of genomic data that any bin can index.

See Also:

Constant Field Values

LEVEL_STARTS

public static final int[] LEVEL_STARTS

What is the starting bin for each level?

MAX_BINS

public static final int MAX_BINS

Reports the maximum number of bins that can appear in a binning index.

See Also:

Constant Field Values

MAX_LINEAR_INDEX_SIZE

public static final int MAX_LINEAR_INDEX_SIZE

UNSET_GENOMIC_LOCATION

public static final int UNSET_GENOMIC_LOCATION

E.g. for a SAMRecord with no genomic coordinate.

See Also:

Constant Field Values

Constructor Detail

GenomicIndexUtil

public GenomicIndexUtil()

Method Detail

regionToBin

public static int regionToBin(int beg,
                              int end)

calculate the bin given an alignment in [beg,end) Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "

Parameters:

beg - 0-based start of read (inclusive)

end - 0-based end of read (exclusive)

regionToBins

public static java.util.BitSet regionToBins(int startPos,
                                            int endPos)

Get candidate bins for the specified region

Parameters:

startPos - 1-based start of target region, inclusive.

endPos - 1-based end of target region, inclusive.

Returns:

bit set for each bin that may contain SAMRecords in the target region.