JavascriptSamRecordFilter (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.filter.AbstractJavascriptFilter<SAMFileHeader,SAMRecord>
- - htsjdk.samtools.filter.JavascriptSamRecordFilter

All Implemented Interfaces:

SamRecordFilter
```
public class JavascriptSamRecordFilter
extends AbstractJavascriptFilter<SAMFileHeader,SAMRecord>
implements SamRecordFilter
```
javascript based read filter The script puts the following variables in the script context: - 'record' a SamRecord ( https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/ SAMRecord.java ) - 'header' ( https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/ SAMFileHeader.java )

Field Summary
- Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
  bindings, DEFAULT_HEADER_KEY

Constructor Summary

Constructors
Constructor	Description
`JavascriptSamRecordFilter(File scriptFile, SAMFileHeader header)`	constructor using a javascript File
`JavascriptSamRecordFilter(Reader scriptReader, SAMFileHeader header)`	constructor using a java.io.Reader
`JavascriptSamRecordFilter(String scriptExpression, SAMFileHeader header)`	constructor using a javascript expression

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`filterOut(SAMRecord record)`	read is filtered out if the javascript program returns false
`boolean`	`filterOut(SAMRecord first, SAMRecord second)`	return true of both records are filteredOut (AND)
`String`	`getRecordKey()`	returns key used for record binding

Methods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
accept, getHeaderKey

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

- Constructor Detail
  - JavascriptSamRecordFilter
```
public JavascriptSamRecordFilter(File scriptFile,
                                 SAMFileHeader header)
                          throws IOException
```
    constructor using a javascript File
    
    Parameters:
    
    scriptFile - the javascript file to be compiled
    
    header - the SAMHeader
    
    Throws:
    
    IOException
  - JavascriptSamRecordFilter
```
public JavascriptSamRecordFilter(String scriptExpression,
                                 SAMFileHeader header)
```
    constructor using a javascript expression
    
    Parameters:
    
    scriptExpression - the javascript expression to be compiled
    
    header - the SAMHeader
  - JavascriptSamRecordFilter
```
public JavascriptSamRecordFilter(Reader scriptReader,
                                 SAMFileHeader header)
```
    constructor using a java.io.Reader
    
    Parameters:
    
    scriptReader - the javascript reader to be compiled. will be closed
    
    header - the SAMHeader
- Method Detail
  - filterOut
```
public boolean filterOut(SAMRecord first,
                         SAMRecord second)
```
    return true of both records are filteredOut (AND)
    
    Specified by:
    
    filterOut in interface SamRecordFilter
    
    Parameters:
    
    first - the first SAMRecord to evaluate
    
    second - the second SAMRecord to evaluate
    
    Returns:
    
    true if the pair of records matches filter, otherwise false
  - filterOut
```
public boolean filterOut(SAMRecord record)
```
    read is filtered out if the javascript program returns false
    
    Specified by:
    
    filterOut in interface SamRecordFilter
    
    Parameters:
    
    record - the SAMRecord to evaluate
    
    Returns:
    
    true if the SAMRecord matches the filter, otherwise false
  - getRecordKey
```
public String getRecordKey()
```
    Description copied from class: AbstractJavascriptFilter
    
    returns key used for record binding
    
    Specified by:
    
    getRecordKey in class AbstractJavascriptFilter<SAMFileHeader,SAMRecord>

Class JavascriptSamRecordFilter

Field Summary

Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

Methods inherited from class java.lang.Object

Constructor Detail

JavascriptSamRecordFilter

JavascriptSamRecordFilter

JavascriptSamRecordFilter

Method Detail

filterOut

filterOut

getRecordKey