Package org.snpsift.annotate
Class DbVcfTabix
- java.lang.Object
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- org.snpsift.annotate.DbVcf
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- org.snpsift.annotate.DbVcfTabix
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
chrPrepend
protected htsjdk.tribble.readers.TabixReader
tabixReader
protected org.snpeff.fileIterator.VcfFileIterator
vcf
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Fields inherited from class org.snpsift.annotate.DbVcf
dbFileName, debug, vcfHeader, verbose
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Constructor Summary
Constructors Constructor Description DbVcfTabix(java.lang.String dbFileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Close database, free resourcesprotected boolean
initTabix(java.lang.String fileName)
Initialize tabix readervoid
open()
Open database annotation filejava.util.List<org.snpeff.vcf.VariantVcfEntry>
query(org.snpeff.interval.Variant variant)
Find matching entries in the database-
Methods inherited from class org.snpsift.annotate.DbVcf
getVcfHeader, setDebug, setVerbose
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Method Detail
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close
public void close()
Description copied from interface:DbMarker
Close database, free resources
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initTabix
protected boolean initTabix(java.lang.String fileName)
Initialize tabix reader
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open
public void open()
Open database annotation file
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query
public java.util.List<org.snpeff.vcf.VariantVcfEntry> query(org.snpeff.interval.Variant variant)
Description copied from class:DbVcf
Find matching entries in the database
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