Package htsjdk.samtools
Class GenomicIndexUtil
- java.lang.Object
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- htsjdk.samtools.GenomicIndexUtil
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public class GenomicIndexUtil extends Object
Constants and methods used by BAM and Tribble indices
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Field Summary
Fields 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.
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Constructor Summary
Constructors Constructor Description GenomicIndexUtil()
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Method Summary
All Methods Static Methods Concrete Methods 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
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Field Detail
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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
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LEVEL_STARTS
public static final int[] LEVEL_STARTS
What is the starting bin for each level?
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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
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MAX_LINEAR_INDEX_SIZE
public static final int MAX_LINEAR_INDEX_SIZE
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UNSET_GENOMIC_LOCATION
public static final int UNSET_GENOMIC_LOCATION
E.g. for a SAMRecord with no genomic coordinate.- See Also:
- Constant Field Values
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Method Detail
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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)
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regionToBins
public static 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.
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