- All Implemented Interfaces:
DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
public class DbVcfMem
extends DbVcf
Loads a VCF file into memory.
WARNING: This is used only for testing and debugging purposes and should
never be used in production!
- Author:
- pcingola
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Field Summary
Fields
static final int
static final int
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Constructor Summary
Constructors
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Method Summary
void
Close database, free resources
void
Open database annotation file
List<org.snpeff.vcf.VariantVcfEntry>
query(org.snpeff.interval.Variant variant)
Find matching entries in the database
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Field Details
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SHOW
public static final int SHOW
- See Also:
-
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SHOW_LINES
public static final int SHOW_LINES
- See Also:
-
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Constructor Details
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DbVcfMem
public DbVcfMem(String dbFileName)
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Method Details
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close
public void close()
Description copied from interface: DbMarker
Close database, free resources
- Specified by:
close
in interface DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
- Specified by:
close
in class DbVcf
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open
public void open()
Open database annotation file
- Specified by:
open
in interface DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
- Specified by:
open
in class DbVcf
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query
public List<org.snpeff.vcf.VariantVcfEntry> query(org.snpeff.interval.Variant variant)
Description copied from class: DbVcf
Find matching entries in the database
- Specified by:
query
in interface DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
- Specified by:
query
in class DbVcf