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