Package org.snpsift.annotate
Class DbVcfSorted
- java.lang.Object
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- org.snpsift.annotate.DbVcf
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- org.snpsift.annotate.DbVcfSorted
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- All Implemented Interfaces:
DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
public class DbVcfSorted extends DbVcf
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed. Each VCF entry should be sorted according to position (as the VCF norm specifies). Chromosome order does not matter (e.g. all entries for chr10 can be before entries for chr2). But entries for the same chromosome should be together. Note: Old VCF specifications did not require VCF files to be sorted.- Author:
- pcingola
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Field Summary
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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 DbVcfSorted(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 resourcesvoid
open()
Open VCF database annotation filejava.util.List<org.snpeff.vcf.VariantVcfEntry>
query(org.snpeff.interval.Variant variant)
Find matching entries in the databasevoid
setMaxBlockSize(int maxBlockSize)
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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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open
public void open()
Open VCF 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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setMaxBlockSize
public void setMaxBlockSize(int maxBlockSize)
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