java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric

Enclosing class:

ExtractIlluminaBarcodes
```
public static class ExtractIlluminaBarcodes.BarcodeMetric
extends htsjdk.samtools.metrics.MetricBase
```
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.

Field Summary

Fields
Modifier and Type	Field	Description
`String`	`BARCODE`	The barcode (from the set of expected barcodes) for which the following metrics apply.
`String`	`BARCODE_NAME`	The barcode name.
`String`	`BARCODE_WITHOUT_DELIMITER`
`protected byte[][]`	`barcodeBytes`
`String`	`LIBRARY_NAME`	The name of the library
`long`	`ONE_MISMATCH_MATCHES`	The number of all reads matching this barcode that matched with 1 error or no-call.
`double`	`PCT_MATCHES`	The fraction of all reads in the lane that matched to this barcode.
`long`	`PERFECT_MATCHES`	The number of all reads matching this barcode that matched with 0 errors or no-calls.
`double`	`PF_NORMALIZED_MATCHES`	The "normalized" matches to each barcode.
`long`	`PF_ONE_MISMATCH_MATCHES`	The number of PF reads matching this barcode that matched with 1 error or no-call.
`double`	`PF_PCT_MATCHES`	The fraction of PF reads in the lane that matched to this barcode.
`long`	`PF_PERFECT_MATCHES`	The number of PF reads matching this barcode that matched with 0 errors or no-calls.
`double`	`PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT`	The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode.
`long`	`PF_READS`	The number of PF reads matching this barcode (always less than or equal to READS).
`double`	`RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT`	The rate of all reads matching this barcode to all reads matching the most prevelant barcode.
`long`	`READS`	The total number of reads matching the barcode.

Constructor Summary

Constructors
Constructor	Description
`BarcodeMetric()`	This ctor is necessary for when reading metrics from file
`BarcodeMetric(String barcodeName, String libraryName, String barcodeDisplay, String[] barcodeSeqs)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static ExtractIlluminaBarcodes.BarcodeMetric`	`copy(ExtractIlluminaBarcodes.BarcodeMetric metric)`	Creates a copy of metric initialized with only non-accumulated and non-calculated values set
`void`	`merge(ExtractIlluminaBarcodes.BarcodeMetric metric)`	Adds the non-calculated

Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString

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

- Field Detail
  - BARCODE
```
public String BARCODE
```
    The barcode (from the set of expected barcodes) for which the following metrics apply. Note that the "symbolic" barcode of NNNNNN is used to report metrics for all reads that do not match a barcode.
  - BARCODE_WITHOUT_DELIMITER
```
public String BARCODE_WITHOUT_DELIMITER
```
  - BARCODE_NAME
```
public String BARCODE_NAME
```
    The barcode name.
  - LIBRARY_NAME
```
public String LIBRARY_NAME
```
    The name of the library
  - READS
```
public long READS
```
    The total number of reads matching the barcode.
  - PF_READS
```
public long PF_READS
```
    The number of PF reads matching this barcode (always less than or equal to READS).
  - PERFECT_MATCHES
```
public long PERFECT_MATCHES
```
    The number of all reads matching this barcode that matched with 0 errors or no-calls.
  - PF_PERFECT_MATCHES
```
public long PF_PERFECT_MATCHES
```
    The number of PF reads matching this barcode that matched with 0 errors or no-calls.
  - ONE_MISMATCH_MATCHES
```
public long ONE_MISMATCH_MATCHES
```
    The number of all reads matching this barcode that matched with 1 error or no-call.
  - PF_ONE_MISMATCH_MATCHES
```
public long PF_ONE_MISMATCH_MATCHES
```
    The number of PF reads matching this barcode that matched with 1 error or no-call.
  - PCT_MATCHES
```
public double PCT_MATCHES
```
    The fraction of all reads in the lane that matched to this barcode.
  - RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
```
public double RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
```
    The rate of all reads matching this barcode to all reads matching the most prevelant barcode. For the most prevelant barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes.
  - PF_PCT_MATCHES
```
public double PF_PCT_MATCHES
```
    The fraction of PF reads in the lane that matched to this barcode.
  - PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
```
public double PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT
```
    The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode. For the most prevelant barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation of PF reads between barcodes.
  - PF_NORMALIZED_MATCHES
```
public double PF_NORMALIZED_MATCHES
```
    The "normalized" matches to each barcode. This is calculated as the number of pf reads matching this barcode over the sum of all pf reads matching any barcode (excluding orphans). If all barcodes are represented equally this will be 1.
  - barcodeBytes
```
protected byte[][] barcodeBytes
```
- Constructor Detail
  - BarcodeMetric
```
public BarcodeMetric(String barcodeName,
                     String libraryName,
                     String barcodeDisplay,
                     String[] barcodeSeqs)
```
  - BarcodeMetric
```
public BarcodeMetric()
```
    This ctor is necessary for when reading metrics from file
- Method Detail
  - copy
```
public static ExtractIlluminaBarcodes.BarcodeMetric copy(ExtractIlluminaBarcodes.BarcodeMetric metric)
```
    Creates a copy of metric initialized with only non-accumulated and non-calculated values set
  - merge
```
public void merge(ExtractIlluminaBarcodes.BarcodeMetric metric)
```
    Adds the non-calculated
    
    Parameters:
    
    metric -

Class ExtractIlluminaBarcodes.BarcodeMetric

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

BARCODE

BARCODE_WITHOUT_DELIMITER

BARCODE_NAME

LIBRARY_NAME

READS

PF_READS

PERFECT_MATCHES

PF_PERFECT_MATCHES

ONE_MISMATCH_MATCHES

PF_ONE_MISMATCH_MATCHES

PCT_MATCHES

RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT

PF_PCT_MATCHES

PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT

PF_NORMALIZED_MATCHES

barcodeBytes

Constructor Detail

BarcodeMetric

BarcodeMetric

Method Detail

copy

merge