picard.illumina

Class ExtractIlluminaBarcodes.BarcodeMetric

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 and Description
java.lang.String	BARCODE The barcode (from the set of expected barcodes) for which the following metrics apply.
java.lang.String	BARCODE_NAME
protected byte[][]	barcodeBytes
java.lang.String	LIBRARY_NAME
int	ONE_MISMATCH_MATCHES The number of all reads matching this barcode that matched with 1 error or no-call.
double	PCT_MATCHES The percentage of all reads in the lane that matched to this barcode.
int	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.
int	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 percentage of PF reads in the lane that matched to this barcode.
int	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.
int	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.
int	READS The total number of reads matching the barcode.

Constructor Summary

Constructors

Constructor and Description
BarcodeMetric() This ctor is necessary for when reading metrics from file
BarcodeMetric(java.lang.String barcodeName, java.lang.String libraryName, java.lang.String barcodeDisplay, java.lang.String[] barcodeSeqs)

Method Summary

Modifier and Type	Method and 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 java.lang.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_NAME

public java.lang.String BARCODE_NAME

LIBRARY_NAME

public java.lang.String LIBRARY_NAME

READS

public int READS

The total number of reads matching the barcode.

PF_READS

public int PF_READS

The number of PF reads matching this barcode (always less than or equal to READS).

PERFECT_MATCHES

public int PERFECT_MATCHES

The number of all reads matching this barcode that matched with 0 errors or no-calls.

PF_PERFECT_MATCHES

public int PF_PERFECT_MATCHES

The number of PF reads matching this barcode that matched with 0 errors or no-calls.

ONE_MISMATCH_MATCHES

public int ONE_MISMATCH_MATCHES

The number of all reads matching this barcode that matched with 1 error or no-call.

PF_ONE_MISMATCH_MATCHES

public int 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 percentage 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 percentage 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(java.lang.String barcodeName,
                     java.lang.String libraryName,
                     java.lang.String barcodeDisplay,
                     java.lang.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 -