Package org.snpsift.annotate
Class VcfIndexTree
- java.lang.Object
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- org.snpsift.annotate.VcfIndexTree
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- All Implemented Interfaces:
java.lang.Iterable<org.snpeff.interval.Marker>
,org.snpeff.interval.tree.Itree
public class VcfIndexTree extends java.lang.Object implements org.snpeff.interval.tree.Itree
Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays. Nodes are referenced by index in the array- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
COLLAPSE_MAX_NUM_ENTRIES
static int
DEFAULT_MAX_BLOCK_SIZE
static int
INITIAL_CAPACITY
static int
MAX_DIFF_COLLAPSE
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Constructor Summary
Constructors Constructor Description VcfIndexTree()
VcfIndexTree(org.snpeff.fileIterator.VcfFileIterator vcf, VcfIndexDataChromo vcfIndexChromo)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(org.snpeff.interval.Marker interval)
void
add(org.snpeff.interval.Markers markers)
void
build()
java.lang.String
getChromosome()
org.snpeff.interval.Markers
getIntervals()
boolean
isEmpty()
boolean
isInSync()
java.util.Iterator<org.snpeff.interval.Marker>
iterator()
boolean
load(java.io.DataInputStream in)
Read data from input streamvoid
load(java.lang.String fileName, org.snpeff.interval.Genome genome)
org.snpeff.interval.Markers
query(org.snpeff.interval.Interval queryMarker)
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'protected void
query(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'protected void
queryIntersects(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
Query VCF entries intersecting 'marker' at node 'idx'void
save(java.io.DataOutputStream out)
Save to output streamvoid
setDebug(boolean debug)
void
setMaxBlockSize(int maxBlockSize)
void
setVcf(org.snpeff.fileIterator.VcfFileIterator vcf)
void
setVerbose(boolean verbose)
int
size()
org.snpeff.interval.Markers
stab(int point)
java.lang.String
toString()
java.lang.String
toString(int idx)
java.lang.String
toStringAll()
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Field Detail
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COLLAPSE_MAX_NUM_ENTRIES
public static final int COLLAPSE_MAX_NUM_ENTRIES
- See Also:
- Constant Field Values
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DEFAULT_MAX_BLOCK_SIZE
public static final int DEFAULT_MAX_BLOCK_SIZE
- See Also:
- Constant Field Values
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INITIAL_CAPACITY
public static final int INITIAL_CAPACITY
- See Also:
- Constant Field Values
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MAX_DIFF_COLLAPSE
public static final int MAX_DIFF_COLLAPSE
- See Also:
- Constant Field Values
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Constructor Detail
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VcfIndexTree
public VcfIndexTree()
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VcfIndexTree
public VcfIndexTree(org.snpeff.fileIterator.VcfFileIterator vcf, VcfIndexDataChromo vcfIndexChromo)
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Method Detail
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add
public void add(org.snpeff.interval.Marker interval)
- Specified by:
add
in interfaceorg.snpeff.interval.tree.Itree
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add
public void add(org.snpeff.interval.Markers markers)
- Specified by:
add
in interfaceorg.snpeff.interval.tree.Itree
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build
public void build()
- Specified by:
build
in interfaceorg.snpeff.interval.tree.Itree
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getChromosome
public java.lang.String getChromosome()
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getIntervals
public org.snpeff.interval.Markers getIntervals()
- Specified by:
getIntervals
in interfaceorg.snpeff.interval.tree.Itree
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isEmpty
public boolean isEmpty()
- Specified by:
isEmpty
in interfaceorg.snpeff.interval.tree.Itree
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isInSync
public boolean isInSync()
- Specified by:
isInSync
in interfaceorg.snpeff.interval.tree.Itree
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iterator
public java.util.Iterator<org.snpeff.interval.Marker> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<org.snpeff.interval.Marker>
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load
public boolean load(java.io.DataInputStream in)
Read data from input stream- Returns:
- true on success
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load
public void load(java.lang.String fileName, org.snpeff.interval.Genome genome)
- Specified by:
load
in interfaceorg.snpeff.interval.tree.Itree
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query
public org.snpeff.interval.Markers query(org.snpeff.interval.Interval queryMarker)
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'- Specified by:
query
in interfaceorg.snpeff.interval.tree.Itree
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query
protected void query(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
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queryIntersects
protected void queryIntersects(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
Query VCF entries intersecting 'marker' at node 'idx'
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save
public void save(java.io.DataOutputStream out)
Save to output stream
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setDebug
public void setDebug(boolean debug)
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setMaxBlockSize
public void setMaxBlockSize(int maxBlockSize)
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setVcf
public void setVcf(org.snpeff.fileIterator.VcfFileIterator vcf)
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setVerbose
public void setVerbose(boolean verbose)
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size
public int size()
- Specified by:
size
in interfaceorg.snpeff.interval.tree.Itree
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stab
public org.snpeff.interval.Markers stab(int point)
- Specified by:
stab
in interfaceorg.snpeff.interval.tree.Itree
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toString
public java.lang.String toString(int idx)
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toStringAll
public java.lang.String toStringAll()
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