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	binTolevel(int bin) Return the binning index level for the given bin.
static java.lang.String	getBinSummaryString(int bin) Return a summary string describing the bin level, level size, and genomic territory covered by the bin.
static int	levelToSize(int level) Return the binning index bin size for bins in the given bin.
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 int	regionToBin(int beg, int end, int minShift, int binDepth) 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
static java.util.BitSet	regionToBins(int startPos, int endPos, int minShift, int binDepth) 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

binTolevel

public static int binTolevel(int bin)

Return the binning index level for the given bin. Assumes a .bai/.tbi binning scheme (not for use with .csi).

Parameters:

bin - the bin to analyze

Returns:

the binning index level for the given bin

levelToSize

public static int levelToSize(int level)

Return the binning index bin size for bins in the given bin. Assumes a .bai/.tbi binning scheme (not for use with .csi).

Parameters:

level - the level to analyze

Returns:

the size for a bin at the given level

getBinSummaryString

public static java.lang.String getBinSummaryString(int bin)

Return a summary string describing the bin level, level size, and genomic territory covered by the bin. For use as debug output.

Parameters:

bin - input bin

Returns:

A summary string describing the bin. The intended use is for debug output - the string is not intended to be machine readable/parsed and is subject to change.

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)

regionToBin

public static int regionToBin(int beg,
                              int end,
                              int minShift,
                              int binDepth)

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)

minShift - minimum bin width (2^minShift)

binDepth - number of levels in the binning scheme (including bin 0)

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.

regionToBins

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

Get candidate bins for the specified region

Parameters:

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

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

minShift - minimum bin width (2^minShift).

binDepth - number of levels in the binning scheme (including bin 0).

Returns:

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