Package org.snpsift.annotate
Class VcfIndexDataChromo
java.lang.Object
org.snpsift.annotate.VcfIndexDataChromo
Represents a set of VCF entries stored in an (uncompressed) file
All entries belong to the same chromosome
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionVcfIndexDataChromo
(org.snpeff.interval.Genome genome) VcfIndexDataChromo
(org.snpeff.interval.Genome genome, String chromosome) -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(int start, int end, long fileIdx) Add [start, end] => filePoslong
fileSize
(int startIdx, int endIdx) File size between startIdx and endIdx inclusiveint
getEnd
(int idx) long
getFilePosEnd
(int idx) long
getFilePosStart
(int idx) int
getStart
(int idx) boolean
intersects
(int idx, int pos) Does interval at position 'idx' intersect positions 'pos'?boolean
intersects
(int idx, org.snpeff.interval.Marker marker) Does interval at position 'idx' intersect 'marker'?org.snpeff.interval.Marker
marker
(int idx) Create a marker form data at position 'idx'void
setFilePosEnd
(long filePosEnd) int
size()
toString()
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Field Details
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INITIAL_CAPACITY
public static final int INITIAL_CAPACITY- See Also:
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Constructor Details
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VcfIndexDataChromo
public VcfIndexDataChromo(org.snpeff.interval.Genome genome) -
VcfIndexDataChromo
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Method Details
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add
public void add(int start, int end, long fileIdx) Add [start, end] => filePos -
fileSize
public long fileSize(int startIdx, int endIdx) File size between startIdx and endIdx inclusive -
getChromosome
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getEnd
public int getEnd(int idx) -
getFilePosEnd
public long getFilePosEnd(int idx) -
getFilePosStart
public long getFilePosStart(int idx) -
getStart
public int getStart(int idx) -
intersects
public boolean intersects(int idx, int pos) Does interval at position 'idx' intersect positions 'pos'? -
intersects
public boolean intersects(int idx, org.snpeff.interval.Marker marker) Does interval at position 'idx' intersect 'marker'? -
marker
public org.snpeff.interval.Marker marker(int idx) Create a marker form data at position 'idx' -
setFilePosEnd
public void setFilePosEnd(long filePosEnd) -
size
public int size() -
toString
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