picard.illumina.quality

Class CollectHiSeqXPfFailMetrics.ReadClassifier

java.lang.Object

picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier

Enclosing class:

CollectHiSeqXPfFailMetrics

protected static class CollectHiSeqXPfFailMetrics.ReadClassifier
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason

Constructor Summary

Constructors

Constructor and Description
ReadClassifier(ReadData read) Heart of CLP.

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

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.