Package org.snpsift.annotate
Class VcfIndex
- java.lang.Object
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- org.snpsift.annotate.VcfIndex
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public class VcfIndex extends java.lang.Object
An index for a VCF file- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
INDEX_EXT
static int
INDEX_FORMAT_VERSION
static int
SHOW_EVERY
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Constructor Summary
Constructors Constructor Description VcfIndex(java.lang.String fileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(org.snpeff.vcf.VcfEntry ve, long filePos)
Add an interval parse from 'line'void
close()
Close file and free memoryorg.snpeff.interval.Genome
getGenome()
VcfIndexDataChromo
getOrCreate(java.lang.String chromosome)
Get IntervalFileChromo by chromosome name.VcfIndexTree
getTree(java.lang.String chromosome)
org.snpeff.fileIterator.VcfFileIterator
getVcf()
VcfIndexDataChromo
getVcfIndexChromo(java.lang.String chromosome)
void
index()
Load or create indexprotected void
loadIndex(java.lang.String indexFile)
Load index form a filevoid
open()
Open fileorg.snpeff.interval.Markers
query(org.snpeff.interval.Marker marker)
Query interval forestorg.snpeff.vcf.VcfEntry
read(long fileIdx)
Read a VcfEntry at position 'fileIdx'org.snpeff.vcf.VcfEntry
read(MarkerFile markerFile)
Read a VcfEntry referenced by 'markerFile'void
save(java.lang.String indexFile)
Save index filevoid
setDebug(boolean debug)
void
setMaxBlockSize(int maxBlockSize)
void
setVerbose(boolean verbose)
java.lang.String
toString()
java.lang.String
toStringAll()
Show all entries
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Field Detail
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INDEX_FORMAT_VERSION
public static int INDEX_FORMAT_VERSION
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SHOW_EVERY
public static int SHOW_EVERY
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INDEX_EXT
public static final java.lang.String INDEX_EXT
- See Also:
- Constant Field Values
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Method Detail
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add
public void add(org.snpeff.vcf.VcfEntry ve, long filePos)
Add an interval parse from 'line'
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close
public void close()
Close file and free memory
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getGenome
public org.snpeff.interval.Genome getGenome()
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getOrCreate
public VcfIndexDataChromo getOrCreate(java.lang.String chromosome)
Get IntervalFileChromo by chromosome name. Create a new one if it doesn't exists
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getTree
public VcfIndexTree getTree(java.lang.String chromosome)
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getVcf
public org.snpeff.fileIterator.VcfFileIterator getVcf()
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getVcfIndexChromo
public VcfIndexDataChromo getVcfIndexChromo(java.lang.String chromosome)
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index
public void index()
Load or create index
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loadIndex
protected void loadIndex(java.lang.String indexFile)
Load index form a file
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open
public void open()
Open file
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query
public org.snpeff.interval.Markers query(org.snpeff.interval.Marker marker)
Query interval forest
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read
public org.snpeff.vcf.VcfEntry read(long fileIdx)
Read a VcfEntry at position 'fileIdx'
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read
public org.snpeff.vcf.VcfEntry read(MarkerFile markerFile)
Read a VcfEntry referenced by 'markerFile'
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save
public void save(java.lang.String indexFile)
Save index file
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setDebug
public void setDebug(boolean debug)
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setMaxBlockSize
public void setMaxBlockSize(int maxBlockSize)
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringAll
public java.lang.String toStringAll()
Show all entries
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