Package picard.illumina
Class BarcodeMetric
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.illumina.BarcodeMetric
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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
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 librarylong
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 prevalent 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 prevalent barcode.long
READS
The total number of reads matching the barcode.
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Constructor Summary
Constructors Constructor Description BarcodeMetric()
This ctor is necessary for when reading metrics from fileBarcodeMetric(String barcodeName, String libraryName, String barcodeDisplay, String[] barcodeSeqs)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description BarcodeMetric
copy()
Creates a copy of metric initialized with only non-accumulated and non-calculated values setvoid
merge(BarcodeMetric metric)
Adds the non-calculated
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Field Detail
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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.
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BARCODE_WITHOUT_DELIMITER
public String BARCODE_WITHOUT_DELIMITER
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BARCODE_NAME
public String BARCODE_NAME
The barcode name.
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LIBRARY_NAME
public String LIBRARY_NAME
The name of the library
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READS
public long READS
The total number of reads matching the barcode.
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PF_READS
public long PF_READS
The number of PF reads matching this barcode (always less than or equal to READS).
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PERFECT_MATCHES
public long PERFECT_MATCHES
The number of all reads matching this barcode that matched with 0 errors or no-calls.
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PF_PERFECT_MATCHES
public long PF_PERFECT_MATCHES
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
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ONE_MISMATCH_MATCHES
public long ONE_MISMATCH_MATCHES
The number of all reads matching this barcode that matched with 1 error or no-call.
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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.
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PCT_MATCHES
public double PCT_MATCHES
The fraction of all reads in the lane that matched to this barcode.
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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 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.
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PF_PCT_MATCHES
public double PF_PCT_MATCHES
The fraction of PF reads in the lane that matched to this barcode.
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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 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.
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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.
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barcodeBytes
protected byte[][] barcodeBytes
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Method Detail
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copy
public BarcodeMetric copy()
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
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merge
public void merge(BarcodeMetric metric)
Adds the non-calculated
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