Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics.ReadClassifier
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- picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
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- Enclosing class:
- CollectHiSeqXPfFailMetrics
protected static class CollectHiSeqXPfFailMetrics.ReadClassifier extends Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
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Constructor Summary
Constructors Constructor Description ReadClassifier(ReadData read)
Heart of CLP.
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Constructor Detail
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ReadClassifier
public ReadClassifier(ReadData read)
Heart of CLP. This class actually classifies ReadData into the reason why it failed PF classification is based on a small set of titrated flowcells sequenced at the Broad Institute by the Genomics Platform. Three cluster were observed: - numNs~24 and was found only near the boundaries of tiles. it didn't seem to depend on concentration. For this reason it was classified as MISALIGNED - numNs~0 and numQGtTwo<=8 these were found throughout the tiles and _decreased_ in number as the concentration of the library increased Thus it was concluded that these correspond to the EMPTY wells - numNs~0 and numQGtTwo>=12 there were found throughout the tiles and _increased_ in number as the concentration of the library increased Thus it was concluded that these correspond to the POLYCLONAL wells - the remaining reads were few in number the classification for them wasn't clear. Thus they are left as UNKNOWN. We use the length of the read as a parameter and scale the 8 and the 12 accordingly as length/3 and length/2, but in reality this has only been tested on length=24.- Parameters:
read
- The read to classify.
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