PacBioPrimaryMetricsΒΆ

<?xml version="1.0" encoding="utf-8"?>
<?xml-stylesheet type="text/xsl" href="xs3p.xsl"?>
<!--
*******************************************************************************
**
**  File Name: PipeStats.xsd
**             XML schema defining pipeline statistics
**
**  Programmer: Aseneth Lopez, Phil McClueg
**
**  $Id$
**
*******************************************************************************
**  History:
**
**      2010/03/11 pmcclurg - created to correspond to new Functional Specs
**
*******************************************************************************
-->
<xs:schema xmlns="http://pacificbiosciences.com/PacBioPipelineStats.xsd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" targetNamespace="http://pacificbiosciences.com/PacBioPipelineStats.xsd" elementFormDefault="qualified" id="PacBioPipelineStats">
	<xs:import namespace="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" schemaLocation="PacBioBaseDataModel.xsd"/>
	<!--
  
  Movie Metrics and Classification
  
  -->
	<!--
  MovieContext
  -->
	<xs:element name="MovieName" type="xs:string"/>
	<!--
  MovieLength
  -->
	<xs:element name="MovieLength" type="xs:double"/>
	<!--
  NumDroppedFrames
  -->
	<xs:element name="NumFramesDropped" type="xs:double"/>
	<!--
  NumSequencingZmws
  -->
	<xs:element name="NumSequencingZmws" type="xs:double"/>
	<!--
  TraceFileSize
  -->
	<xs:element name="TraceFileSize" type="xs:long"/>
	<!--
  PulseFileSize
  -->
	<xs:element name="PulseFileSize" type="xs:long"/>
	<!--
  BaseFileSize
  -->
	<xs:element name="BaseFileSize" type="xs:long"/>
	<!--
  AdapterDimerFraction
  -->
	<xs:element name="AdapterDimerFraction" type="xs:double"/>
	<!--
  ShortInsertFraction
  -->
	<xs:element name="ShortInsertFraction" type="xs:double"/>
	<!--
  FractionFailedZmwClippedLow
  -->
	<xs:element name="FailedZmwClippedLowFraction" type="xs:double"/>
	<!--
  FractionFailedZmwClippedHigh
  -->
	<xs:element name="FailedZmwClippedHighFraction" type="xs:double"/>
	<!--
  TotalBaseFraction
  -->
	<xs:element name="TotalBaseFractionValue" type="xs:double"/>
	<xs:complexType name="TotalBaseFraction">
		<xs:sequence>
			<xs:element ref="TotalBaseFractionValue"/>
		</xs:sequence>
		<xs:attribute name="Channel" type="xs:string" use="required"/>
	</xs:complexType>
	<xs:element name="TotalBaseFractionPerChannel" type="TotalBaseFraction"/>
	<!--
  PkMidCV
  -->
	<xs:element name="PkMidCVValue" type="xs:double"/>
	<xs:complexType name="PkMidCV">
		<xs:sequence>
			<xs:element ref="PkMidCVValue"/>
		</xs:sequence>
		<xs:attribute name="Channel" type="xs:string" use="required"/>
	</xs:complexType>
	<xs:element name="PkMidCVPerChannel" type="PkMidCV"/>
	<!--
  Total number of counts in the sample
  -->
	<xs:element name="SampleSize" type="xs:int">
		<xs:annotation>
			<xs:documentation>Number of data values in the sample</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  Mean of the sample
  -->
	<xs:element name="SampleMean" type="xs:double">
		<xs:annotation>
			<xs:documentation>Mean of the sample</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  Median of the sample
  -->
	<xs:element name="SampleMed" type="xs:double">
		<xs:annotation>
			<xs:documentation>Median of the sample</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  Standard Deviation of the sample
  -->
	<xs:element name="SampleStd" type="xs:double">
		<xs:annotation>
			<xs:documentation>StandardDeviation of the sample</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  95th Percentile of the sample
  -->
	<xs:element name="Sample95thPct" type="xs:double">
		<xs:annotation>
			<xs:documentation>95th Percentile of the sample</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Number of Bins in Histogram 
  -->
	<xs:element name="NumBins" type="xs:int">
		<xs:annotation>
			<xs:documentation>Number of Bins in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Bin Counts in Histogram
  -->
	<xs:element name="BinCount" type="xs:int">
		<xs:annotation>
			<xs:documentation>Bin Counts in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Bin Width in Histogram
  -->
	<xs:element name="BinWidth" type="xs:double">
		<xs:annotation>
			<xs:documentation>Bin Width in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Histogram outlier minimum value 
  -->
	<xs:element name="MinOutlierValue" type="xs:double">
		<xs:annotation>
			<xs:documentation>Minimum Outlier Value in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
   Histogram minimum bin value (less outliers)
  -->
	<xs:element name="MinBinValue" type="xs:double">
		<xs:annotation>
			<xs:documentation>Minimum Value (less outliers) in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  
  Histogram maximum bin value (less outliers)
  
  -->
	<xs:element name="MaxBinValue" type="xs:double">
		<xs:annotation>
			<xs:documentation>Maximum Value (less outliers) in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Histogram outlier maximum value 
  -->
	<xs:element name="MaxOutlierValue" type="xs:double">
		<xs:annotation>
			<xs:documentation>Maximum Value in Histogram</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  "Human-Readable" description of movie metric
  -->
	<xs:element name="MetricDescription" type="xs:string">
		<xs:annotation>
			<xs:documentation>Description of metric</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!--
  Bin Labels for discrete distributions
  -->
	<xs:element name="BinLabel" type="xs:string">
		<xs:annotation>
			<xs:documentation>Bin Label for Discrete Distribution</xs:documentation>
		</xs:annotation>
	</xs:element>
	<!-- 
  Continuous distribution class
	<xs:complexType name="ContinuousDist">
		<xs:sequence>
			<xs:element ref="SampleSize"/>
			<xs:element ref="SampleMean"/>
			<xs:element ref="SampleMed"/>
			<xs:element ref="SampleStd"/>
			<xs:element ref="Sample95thPct"/>
			<xs:element ref="NumBins"/>
			<xs:element ref="BinCount" minOccurs="1" maxOccurs="unbounded"/>
			<xs:element ref="BinWidth"/>
			<xs:element ref="MinOutlierValue"/>
			<xs:element ref="MinBinValue"/>
			<xs:element ref="MaxBinValue"/>
			<xs:element ref="MaxOutlierValue"/>
			<xs:element ref="MetricDescription"/>
		</xs:sequence>
		<xs:attribute name="Channel" type="xs:string"/>
	</xs:complexType>  -->
	<!-- 
  Discrete distribution class
	<xs:complexType name="DiscreteDist">
		<xs:sequence>
			<xs:element ref="NumBins"/>
			<xs:element ref="BinCount" minOccurs="1" maxOccurs="unbounded"/>
			<xs:element ref="MetricDescription"/>
			<xs:element ref="BinLabel" minOccurs="1" maxOccurs="unbounded"/>
		</xs:sequence>
	</xs:complexType>  -->
	<!--
  Time series (for time-dependent metrics)
	<xs:complexType name="TimeSeries">
		<xs:sequence>
			<xs:element name="TimeUnits" type="xs:string"/>
			<xs:element name="ValueUnits" type="xs:string"/>
			<xs:element name="StartTime" type="xs:float"/>
			<xs:element name="MeasInterval" type="xs:float"/>
			<xs:element name="Val" type="xs:float" minOccurs="0" maxOccurs="unbounded"/>
		</xs:sequence>
	</xs:complexType>  -->
	<!--
  Specific Distributions
  -->
	<!--
  Control Read Length Distribution
  -->
	<xs:element name="ControlReadLenDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Control Read Quality Distribution 
  -->
	<xs:element name="ControlReadQualDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Baseline Level Distribution - all holes
  -->
	<xs:element name="BaselineLevelDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Baseline Standard Deviation Distribution - all holes
  -->
	<xs:element name="BaselineStdDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Movie Read Quality Distribution - all holes
  -->
	<xs:element name="MovieReadQualDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Productivity Distribution - all holes
  -->
	<xs:element name="ProdDist" type="pbbase:StatsDiscreteDistType"/>
	<!--
  ReadType Distribution
  -->
	<xs:element name="ReadTypeDist" type="pbbase:StatsDiscreteDistType"/>
	<!--
  Pulse Rate Distribution - productive holes
  -->
	<xs:element name="PulseRateDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Mean Pulse Width Distribution - productive holes
  -->
	<xs:element name="PulseWidthDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Base Rate (global) Distribution - productive holes, HQ regions
  -->
	<xs:element name="BaseRateDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Mean Base Width Distribution - productive holes, HQ regions
  -->
	<xs:element name="BaseWidthDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Mean Base IPD Distribution - productive holes, HQ regions
  -->
	<xs:element name="BaseIpdDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Local Base Rate Distribution - productive holes, HQ regions.
  I.e., an estimate of the polymerase rate, exclusing pauses.
  -->
	<xs:element name="LocalBaseRateDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Number of unfiltered basecalls Distribution - productive holes
  -->
	<xs:element name="NumUnfilteredBasecallsDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Polymerase Read Length Distribution - productive holes
  -->
	<xs:element name="ReadLenDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Polymerase Read Quality Distribution - productive holes
  -->
	<xs:element name="ReadQualDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Distribution of the ratio (Polymerase Read Len)/(Num Unfiltered Basecalls)
  -->
	<xs:element name="HqBaseFractionDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Polymerase Read-Mean Base Quality Value Distribution - productive holes
  -->
	<xs:element name="RmBasQvDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Best Estimate (Insert) Read Length Distribution
  -->
	<xs:element name="InsertReadLenDist" type="pbbase:StatsContinuousDistType"/>
	<!--
   Best Estimate (Insert) Read Quality (Predicted Accuracy) Distribution
  -->
	<xs:element name="InsertReadQualDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Local Yield Distribution - % of productive holes locally
  -->
	<xs:element name="LocalYieldDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Local Snr Distribution - snr per channel locally
  -->
	<xs:element name="LocalSnrDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Trace Clipped Fraction Distribution - Total % traces clipped per channel
  -->
	<xs:element name="TraceClippedFractionDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Trace Low Clipped Fraction Distribution - % traces clipped low per channel
  -->
	<xs:element name="TraceLowClippedFractionDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Trace High Clipped Fraction Distribution - % traces clipped high per channel
  -->
	<xs:element name="TraceHighClippedFractionDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Pausiness Distribution - % ipds above a threshold
  -->
	<xs:element name="PausinessDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Adapter Dimer Distribution - % distribution of mean insert length
  -->
	<xs:element name="MedianInsertDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  PkMid CV Distribution - % distribution of coefficient of variation of PkMid
  -->
	<xs:element name="PkMidCVDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  SNR Distribution - productive holes
  -->
	<xs:element name="SnrDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  HQ Region SNR Distribution - robust estimate of SNR distribution over productive holes
  -->
	<xs:element name="HqRegionSnrDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  HqBasPkMid Distribution - productive holes
  -->
	<xs:element name="HqBasPkMidDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  BaselineLevelSequencing Distribution - productive holes
  -->
	<xs:element name="BaselineLevelSequencingDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  BaselineLevelAntihole Distribution - productive holes
  -->
	<xs:element name="BaselineLevelAntiholeDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  BaselineLevelAntimirror Distribution - productive holes
  -->
	<xs:element name="BaselineLevelAntimirrorDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  BaselineLevelFiducial Distribution - productive holes
  -->
	<xs:element name="BaselineLevelFiducialDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  Subsystem Failure Metrics, Added in Software v1.3.1
  -->
	<xs:element name="MaxPauseFractionVsT" type="xs:double"/>
	<xs:element name="TMaxPauseFraction" type="xs:int"/>
	<xs:element name="MaxSlopePauseFractionVsT" type="xs:double"/>
	<xs:element name="TMaxSlopePauseFraction" type="xs:int"/>
	<xs:element name="MaxBaseRateRatioVsT" type="xs:double"/>
	<xs:element name="TMaxBaseRateRatio" type="xs:int"/>
	<xs:element name="MaxSlopeBaseRateRatioVsT" type="xs:double"/>
	<xs:element name="TMaxSlopeBaseRateRatio" type="xs:int"/>
	<xs:element name="SgnMaxSlopeBaseRateRatio" type="xs:int"/>
	<xs:element name="BaseRateChngStrtToEnd" type="xs:double"/>
	<xs:element name="YieldCvOverRegions" type="xs:double"/>
	<xs:element name="YieldChngCntrToEdge" type="xs:double"/>
	<xs:element name="SnrRatioEdgeToCntr_0" type="xs:double"/>
	<xs:element name="SnrRatioEdgeToCntr_2" type="xs:double"/>
	<xs:element name="PauseFractionVsT" type="pbbase:StatsTimeSeriesType"/>
	<xs:element name="BaseRateRatioVsT" type="pbbase:StatsTimeSeriesType"/>
	<!--
  Other v1.3.1 Metric Additions
  -->
	<xs:element name="IsReadsFraction" type="xs:double"/>
	<!--
  v2.0 Additions - spectral diagnostics
  -->
	<xs:element name="SpectralDiagRRDist" type="pbbase:StatsContinuousDistType"/>
	<!--
  PipeStats class for PipelineStats XML
  -->
	<xs:element name="PipeStats">
		<xs:complexType>
			<xs:sequence>
				<xs:element ref="MovieName" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="MovieLength" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="NumFramesDropped" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="NumSequencingZmws" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TraceFileSize" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="PulseFileSize" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseFileSize" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="AdapterDimerFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="ShortInsertFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="IsReadsFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="FailedZmwClippedLowFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="FailedZmwClippedHighFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="ControlReadLenDist" minOccurs="0" maxOccurs="1"/>
				<xs:element ref="ControlReadQualDist" minOccurs="0" maxOccurs="1"/>
				<xs:element ref="ProdDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="ReadTypeDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TotalBaseFractionPerChannel" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="PkMidCVPerChannel" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineLevelDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineStdDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="MovieReadQualDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="PulseRateDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="PulseWidthDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseRateDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseWidthDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseIpdDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="LocalBaseRateDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="NumUnfilteredBasecallsDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="ReadLenDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="ReadQualDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="HqBaseFractionDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="RmBasQvDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="InsertReadLenDist" minOccurs="0" maxOccurs="1"/>
				<xs:element ref="InsertReadQualDist" minOccurs="0" maxOccurs="1"/>
				<xs:element ref="LocalYieldDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="LocalSnrDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="TraceClippedFractionDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="TraceLowClippedFractionDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="TraceHighClippedFractionDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="PausinessDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="MedianInsertDist" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="SnrDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="HqRegionSnrDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="HqBasPkMidDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineLevelSequencingDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineLevelAntiholeDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineLevelAntimirrorDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="BaselineLevelFiducialDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="SpectralDiagRRDist" minOccurs="4" maxOccurs="4"/>
				<xs:element ref="MaxPauseFractionVsT" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TMaxPauseFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="MaxSlopePauseFractionVsT" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TMaxSlopePauseFraction" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="MaxBaseRateRatioVsT" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TMaxBaseRateRatio" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="MaxSlopeBaseRateRatioVsT" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="TMaxSlopeBaseRateRatio" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="SgnMaxSlopeBaseRateRatio" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseRateChngStrtToEnd" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="YieldCvOverRegions" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="YieldChngCntrToEdge" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="SnrRatioEdgeToCntr_0" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="SnrRatioEdgeToCntr_2" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="PauseFractionVsT" minOccurs="1" maxOccurs="1"/>
				<xs:element ref="BaseRateRatioVsT" minOccurs="1" maxOccurs="1"/>
			</xs:sequence>
			<xs:attribute name="Version" type="xs:string" use="optional">
				<xs:annotation>
					<xs:documentation>An optional identifier denoting the revision of this particular entity</xs:documentation>
				</xs:annotation>
			</xs:attribute>
		</xs:complexType>
	</xs:element>
</xs:schema>