Package picard.illumina
Class BarcodeMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.BarcodeMetric
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class 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.
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Field Summary
FieldsModifier and TypeFieldDescriptionThe barcode (from the set of expected barcodes) for which the following metrics apply.The barcode name.protected byte[][]
The name of the librarylong
The number of all reads matching this barcode that matched with 1 error or no-call.double
The fraction of all reads in the lane that matched to this barcode.long
The number of all reads matching this barcode that matched with 0 errors or no-calls.double
The "normalized" matches to each barcode.long
The number of PF reads matching this barcode that matched with 1 error or no-call.double
The fraction of PF reads in the lane that matched to this barcode.long
The number of PF reads matching this barcode that matched with 0 errors or no-calls.double
The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode.long
The number of PF reads matching this barcode (always less than or equal to READS).double
The rate of all reads matching this barcode to all reads matching the most prevalent barcode.long
The total number of reads matching the barcode. -
Constructor Summary
ConstructorsConstructorDescriptionThis ctor is necessary for when reading metrics from fileBarcodeMetric
(String barcodeName, String libraryName, String barcodeDisplay, String[] barcodeSeqs) -
Method Summary
Modifier and TypeMethodDescriptioncopy()
Creates a copy of metric initialized with only non-accumulated and non-calculated values setvoid
merge
(BarcodeMetric metric) Adds the non-calculatedMethods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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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
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BARCODE_NAME
The barcode name. -
LIBRARY_NAME
The name of the library -
READS
public long READSThe total number of reads matching the barcode. -
PF_READS
public long PF_READSThe number of PF reads matching this barcode (always less than or equal to READS). -
PERFECT_MATCHES
public long PERFECT_MATCHESThe number of all reads matching this barcode that matched with 0 errors or no-calls. -
PF_PERFECT_MATCHES
public long PF_PERFECT_MATCHESThe number of PF reads matching this barcode that matched with 0 errors or no-calls. -
ONE_MISMATCH_MATCHES
public long ONE_MISMATCH_MATCHESThe number of all reads matching this barcode that matched with 1 error or no-call. -
PF_ONE_MISMATCH_MATCHES
public long PF_ONE_MISMATCH_MATCHESThe number of PF reads matching this barcode that matched with 1 error or no-call. -
PCT_MATCHES
public double PCT_MATCHESThe 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_PCTThe rate of all reads matching this barcode to all reads matching the most prevalent barcode. For the most prevalent 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_MATCHESThe 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_PCTThe rate of PF reads matching this barcode to PF reads matching the most prevalent barcode. For the most prevalent 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_MATCHESThe "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
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Constructor Details
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BarcodeMetric
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BarcodeMetric
public BarcodeMetric()This ctor is necessary for when reading metrics from file
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Method Details
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copy
Creates a copy of metric initialized with only non-accumulated and non-calculated values set -
merge
Adds the non-calculated
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