Package org.snpsift.annotate
Class VcfIndexTree
java.lang.Object
org.snpsift.annotate.VcfIndexTree
- All Implemented Interfaces:
Iterable<org.snpeff.interval.Marker>
,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
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
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Constructor Summary
ConstructorsConstructorDescriptionVcfIndexTree
(org.snpeff.fileIterator.VcfFileIterator vcf, VcfIndexDataChromo vcfIndexChromo) -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(org.snpeff.interval.Marker interval) void
add
(org.snpeff.interval.Markers markers) void
build()
org.snpeff.interval.Markers
boolean
isEmpty()
boolean
isInSync()
Iterator
<org.snpeff.interval.Marker> iterator()
boolean
load
(DataInputStream in) Read data from input streamvoid
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
(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) toString()
toString
(int idx) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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COLLAPSE_MAX_NUM_ENTRIES
public static final int COLLAPSE_MAX_NUM_ENTRIES- See Also:
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DEFAULT_MAX_BLOCK_SIZE
public static final int DEFAULT_MAX_BLOCK_SIZE- See Also:
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INITIAL_CAPACITY
public static final int INITIAL_CAPACITY- See Also:
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MAX_DIFF_COLLAPSE
public static final int MAX_DIFF_COLLAPSE- See Also:
-
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Constructor Details
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VcfIndexTree
public VcfIndexTree() -
VcfIndexTree
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Method Details
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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
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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
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load
Read data from input stream- Returns:
- true on success
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load
- 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' -
queryIntersects
protected void queryIntersects(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results) Query VCF entries intersecting 'marker' at node 'idx' -
save
Save to output stream -
setDebug
public void setDebug(boolean debug) -
setMaxBlockSize
public void setMaxBlockSize(int maxBlockSize) -
setVcf
public void setVcf(org.snpeff.fileIterator.VcfFileIterator vcf) -
setVerbose
public void setVerbose(boolean verbose) -
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
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toString
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toStringAll
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