DemuxUtil

java.lang.Object
- biolockj.util.DemuxUtil

```
public class DemuxUtil
extends Object
```
This utility contains standard methods used to handle multiplexed data.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`BARCODE_CUTOFF` `Config` boolean property "demultiplexer.barcodeCutoff" will look for barcodes in "metadata.barcodeColumn" to exist in this percentage of multiplex file.
`static String`	`BARCODE_USE_REV_COMP` `Config` boolean property "demultiplexer.barcodeRevComp" will use the reverse compliment of "metadata.barcodeColumn" to match sample IDs to sequences.
`static String`	`DEMUX_STRATEGY` `Config` property "demultiplexer.strategy" tells BioLockJ how to match sequences with Sample IDs. Options: barcode_in_header, barcode_in_mapping, barcode_in_seq, id_in_header, do_not_demux. If using barcodes, metadata column "metadata.barcodeColumn" is required.
`static String`	`MAPPING_FILE` `Config` String property "demultiplexer.mapping" lists the path to the mapping file to match sequence headers to barcodes.
`static String`	`OPTION_BARCODE_IN_HEADER` `Config` property "demultiplexer.strategy" option: "barcode_in_header"
`static String`	`OPTION_BARCODE_IN_MAPPING` `Config` property "demultiplexer.strategy" option: "barcode_in_mapping"
`static String`	`OPTION_BARCODE_IN_SEQ` `Config` property "demultiplexer.strategy" option: "barcode_in_seq"
`static String`	`OPTION_DO_NOT_DEMUX` `Config` property "demultiplexer.strategy" option: "do_not_demux"
`static String`	`OPTION_ID_IN_HEADER` `Config` property "demultiplexer.strategy" option: "id_in_header"

Constructor Summary

Constructors
Constructor and Description

DemuxUtil()

Constructors
Constructor and Description
`DemuxUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`barcodeInHeader()` Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence headers.
`static boolean`	`barcodeInMapping()` Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
`static boolean`	`barcodeInSeq()` Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
`static void`	`clearDemuxConfig()` Clear demultiplexer related fields
`static boolean`	`demuxWithBarcode()` Return TRUE if barcode column is defined in the Config file and is populated in the metadata file
`static Boolean`	`doDemux()` Return TRUE if Config is setup to demultiplex the sequence data.
`protected static Map<String,String>`	`getIdMap()` Return the ID map (key=barcodeID, value=sampleId) Print the map to the log file. Barcodes, if used, are located in the metadata column defined by property: `Config`."metadata.barcodeColumn"
`static String`	`getSampleId(List<String> seqLines)` Determine Sample Id by examining the sequence lines. If ="id_in_header", extract the Sample Id from the sequence header via `SeqUtil.getSampleId(String)` If ="barcode_in_header" and the sequence header contains a bar-code in the idMap, return the corresponding SampleID from the idMap. If ="barcode_in_mapping" and the sequence header maps to a bar-code in the idMap, return the corresponding SampleID from the idMap. If ="barcode_in_seq" and the sequence itself begins with a bar-code in the idMap, return the corresponding SampleID from the idMap.
`static boolean`	`hasValidBarcodes()` Check for the existance of the barcode column.
`static boolean`	`sampleIdInHeader()` Return TRUE if Config is setup to demultiplex the sequence data based on Sample IDs in the sequence headers.

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

- Field Detail
  - BARCODE_CUTOFF
```
public static final String BARCODE_CUTOFF
```
    Config boolean property "demultiplexer.barcodeCutoff" will look for barcodes in "metadata.barcodeColumn" to exist in this percentage of multiplex file.
    
    See Also:
    
    Constant Field Values
  - BARCODE_USE_REV_COMP
```
public static final String BARCODE_USE_REV_COMP
```
    Config boolean property "demultiplexer.barcodeRevComp" will use the reverse compliment of "metadata.barcodeColumn" to match sample IDs to sequences.
    
    See Also:
    
    Constant Field Values
  - DEMUX_STRATEGY
```
public static final String DEMUX_STRATEGY
```
    Config property "demultiplexer.strategy" tells BioLockJ how to match sequences with Sample IDs.
    Options: barcode_in_header, barcode_in_mapping, barcode_in_seq, id_in_header, do_not_demux.
    If using barcodes, metadata column "metadata.barcodeColumn" is required.
    
    See Also:
    
    Constant Field Values
  - MAPPING_FILE
```
public static final String MAPPING_FILE
```
    Config String property "demultiplexer.mapping" lists the path to the mapping file to match sequence headers to barcodes. The barcodes found in metadata file "metadata.barcodeColumn" can be used to match sample IDs to sequences.
    
    See Also:
    
    Constant Field Values
  - OPTION_BARCODE_IN_HEADER
```
public static final String OPTION_BARCODE_IN_HEADER
```
    Config property "demultiplexer.strategy" option: "barcode_in_header"
    
    See Also:
    
    Constant Field Values
  - OPTION_BARCODE_IN_MAPPING
```
public static final String OPTION_BARCODE_IN_MAPPING
```
    Config property "demultiplexer.strategy" option: "barcode_in_mapping"
    
    See Also:
    
    Constant Field Values
  - OPTION_BARCODE_IN_SEQ
```
public static final String OPTION_BARCODE_IN_SEQ
```
    Config property "demultiplexer.strategy" option: "barcode_in_seq"
    
    See Also:
    
    Constant Field Values
  - OPTION_DO_NOT_DEMUX
```
public static final String OPTION_DO_NOT_DEMUX
```
    Config property "demultiplexer.strategy" option: "do_not_demux"
    
    See Also:
    
    Constant Field Values
  - OPTION_ID_IN_HEADER
```
public static final String OPTION_ID_IN_HEADER
```
    Config property "demultiplexer.strategy" option: "id_in_header"
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - DemuxUtil
```
public DemuxUtil()
```
- Method Detail
  - barcodeInHeader
```
public static boolean barcodeInHeader()
                               throws ConfigNotFoundException
```
    Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence headers.
    
    Returns:
    
    boolean
    
    Throws:
    
    ConfigNotFoundException - if "demultiplexer.strategy" is undefined
  - barcodeInMapping
```
public static boolean barcodeInMapping()
                                throws ConfigNotFoundException
```
    Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
    
    Returns:
    
    boolean
    
    Throws:
    
    ConfigNotFoundException - if "demultiplexer.strategy" is undefined
  - barcodeInSeq
```
public static boolean barcodeInSeq()
                            throws ConfigNotFoundException
```
    Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
    
    Returns:
    
    boolean
    
    Throws:
    
    ConfigNotFoundException - if "demultiplexer.strategy" is undefined
  - clearDemuxConfig
```
public static void clearDemuxConfig()
```
    Clear demultiplexer related fields
  - demuxWithBarcode
```
public static boolean demuxWithBarcode()
                                throws Exception
```
    Return TRUE if barcode column is defined in the Config file and is populated in the metadata file
    
    Returns:
    
    TRUE or FALSE
    
    Throws:
    
    Exception - if unable to access metadata file or Config
  - doDemux
```
public static Boolean doDemux()
                       throws ConfigNotFoundException
```
    Return TRUE if Config is setup to demultiplex the sequence data.
    
    Returns:
    
    boolean
    
    Throws:
    
    ConfigNotFoundException - if "demultiplexer.strategy" is undefined
  - getSampleId
```
public static String getSampleId(List<String> seqLines)
                          throws Exception
```
    Determine Sample Id by examining the sequence lines.
    If ="id_in_header", extract the Sample Id from the sequence header via SeqUtil.getSampleId(String)
    If ="barcode_in_header" and the sequence header contains a bar-code in the idMap, return the corresponding SampleID from the idMap.
    If ="barcode_in_mapping" and the sequence header maps to a bar-code in the idMap, return the corresponding SampleID from the idMap.
    If ="barcode_in_seq" and the sequence itself begins with a bar-code in the idMap, return the corresponding SampleID from the idMap.
    
    Parameters:
    
    seqLines - List of lines for one fasta or fatsq read
    
    Returns:
    
    Sample ID or null
    
    Throws:
    
    Exception - if propagated from SeqUtil or Config
  - hasValidBarcodes
```
public static boolean hasValidBarcodes()
```
    Check for the existance of the barcode column.
    
    Returns:
    
    Boolean TRUE if barcode column exists and is populated.
  - sampleIdInHeader
```
public static boolean sampleIdInHeader()
```
    Return TRUE if Config is setup to demultiplex the sequence data based on Sample IDs in the sequence headers.
    
    Returns:
    
    boolean
  - getIdMap
```
protected static Map<String,String> getIdMap()
                                      throws Exception
```
    Return the ID map (key=barcodeID, value=sampleId) Print the map to the log file.
    Barcodes, if used, are located in the metadata column defined by property: Config."metadata.barcodeColumn"
    
    Returns:
    
    Id map
    
    Throws:
    
    Exception - if propagated from MetaUtil or Config

Class DemuxUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BARCODE_CUTOFF

BARCODE_USE_REV_COMP

DEMUX_STRATEGY

MAPPING_FILE

OPTION_BARCODE_IN_HEADER

OPTION_BARCODE_IN_MAPPING

OPTION_BARCODE_IN_SEQ

OPTION_DO_NOT_DEMUX

OPTION_ID_IN_HEADER

Constructor Detail

DemuxUtil

Method Detail

barcodeInHeader

barcodeInMapping

barcodeInSeq

clearDemuxConfig

demuxWithBarcode

doDemux

getSampleId

hasValidBarcodes

sampleIdInHeader

getIdMap