VcfAnnotator (SnpEff 5.1 API)

All Superinterfaces:

CommandLine

All Known Implementing Classes:

SnpEffCmdEff, VcfAnnotatorChain
```
public interface VcfAnnotator
extends CommandLine
```
Annotate a VCF file: E.g. add information to INFO column

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`boolean`	`addHeaders(VcfFileIterator vcfFile)`	Add annotation headers to VCF file
`boolean`	`annotate(VcfEntry vcfEntry)`	Annotate a VCF file entry
`boolean`	`annotateFinish(VcfFileIterator vcfFile)`	This method is called after all annotations have been performed.
`boolean`	`annotateInit(VcfFileIterator vcfFile)`	Initialize annotator: This method is called after vcfFile is opened, but before the header is output.
`void`	`setConfig(Config config)`	Set configuration
`void`	`setDebug(boolean debug)`	Set debug mode
`void`	`setVerbose(boolean verbose)`	Set verbose mode

Methods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine
getArgs, parseArgs, run, usage

- Method Detail
  - addHeaders
```
boolean addHeaders(VcfFileIterator vcfFile)
```
    Add annotation headers to VCF file
    
    Returns:
    
    true if OK, false on error
  - annotate
```
boolean annotate(VcfEntry vcfEntry)
```
    Annotate a VCF file entry
    
    Returns:
    
    true if the entry was annotated
  - annotateFinish
```
boolean annotateFinish(VcfFileIterator vcfFile)
```
    This method is called after all annotations have been performed. The vcfFile might have already been closed by this time (i.e. the VcfFileIterator reached the end).
    
    Returns:
    
    true if OK, false on error
  - annotateInit
```
boolean annotateInit(VcfFileIterator vcfFile)
```
    Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.
    
    Returns:
    
    true if OK, false on error
  - setConfig
```
void setConfig(Config config)
```
    Set configuration
  - setDebug
```
void setDebug(boolean debug)
```
    Set debug mode
  - setVerbose
```
void setVerbose(boolean verbose)
```
    Set verbose mode