DbVcfSorted (SnpSift 5.1 API)

java.lang.Object
- org.snpsift.annotate.DbVcf
- - org.snpsift.annotate.DbVcfSorted

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

Field Summary
- Fields inherited from class org.snpsift.annotate.DbVcf
  dbFileName, debug, vcfHeader, verbose

Constructor Summary

Constructors
Constructor Description

DbVcfSorted(java.lang.String dbFileName)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`	Close database, free resources
`void`	`open()`	Open VCF database annotation file
`java.util.List<org.snpeff.vcf.VariantVcfEntry>`	`query(org.snpeff.interval.Variant variant)`	Find matching entries in the database
`void`	`setMaxBlockSize(int maxBlockSize)`

Methods inherited from class org.snpsift.annotate.DbVcf
getVcfHeader, setDebug, setVerbose

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - DbVcfSorted
```
public DbVcfSorted(java.lang.String dbFileName)
```
- Method Detail
  - 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
  - open
```
public void open()
```
    Open VCF database annotation file
    
    Specified by:
    
    open in interface DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
    
    Specified by:
    
    open in class DbVcf
  - 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
    
    Specified by:
    
    query in interface DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>
    
    Specified by:
    
    query in class DbVcf
  - setMaxBlockSize
```
public void setMaxBlockSize(int maxBlockSize)
```