Package htsjdk.samtools
Class LinearIndex
- java.lang.Object
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- htsjdk.samtools.LinearIndex
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public class LinearIndex extends Object
The linear index associated with a given reference in a BAM index.
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Field Summary
Fields Modifier and Type Field Description static int
BAM_LIDX_SHIFT
static int
MAX_LINEAR_INDEX_SIZE
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Constructor Summary
Constructors Constructor Description LinearIndex(int referenceSequence, int indexStart, long[] indexEntries)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static int
convertToLinearIndexOffset(int contigPos)
boolean
equals(Object o)
long
get(int index)
long[]
getIndexEntries()
Direct access to the array.int
getIndexStart()
long
getMinimumOffset(int startPos)
Gets the minimum offset of any alignment start appearing in this index, according to the linear index.int
getReferenceSequence()
int
hashCode()
int
size()
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Field Detail
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MAX_LINEAR_INDEX_SIZE
public static final int MAX_LINEAR_INDEX_SIZE
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BAM_LIDX_SHIFT
public static final int BAM_LIDX_SHIFT
- See Also:
- Constant Field Values
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Method Detail
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getReferenceSequence
public int getReferenceSequence()
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size
public int size()
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get
public long get(int index)
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convertToLinearIndexOffset
public static int convertToLinearIndexOffset(int contigPos)
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getMinimumOffset
public long getMinimumOffset(int startPos)
Gets the minimum offset of any alignment start appearing in this index, according to the linear index.- Parameters:
startPos
- Starting position for this query.- Returns:
- The minimum offset, in chunk format, of any read appearing in this position.
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getIndexEntries
public long[] getIndexEntries()
Direct access to the array. Be careful!- Returns:
- The elements of the linear index.
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getIndexStart
public int getIndexStart()
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