picard.illumina.parser.readers

Class BclQualityEvaluationStrategy

java.lang.Object

picard.illumina.parser.readers.BclQualityEvaluationStrategy

public class BclQualityEvaluationStrategy
extends java.lang.Object

Describes a mechanism for revising and evaluating qualities read from a BCL file. This class accumulates observations about low quality scores that it evaluates, so distinct instances should be used for unrelated sets of BCL readers. The mechanism for revising qualities is not configurable. The qualities that are less than 1 are revised to 1, and other qualities are not affected. This class is thread-safe and a single instance can and should be passed to BclReaders running in separate threads. To replicate the functionality of BclReaders prior to the introduction of this class, create a single instance passing ILLUMINA_ALLEGED_MINIMUM_QUALITY to the constructor, and then call assertMinimumQualities() once the readers finish their work.

Author:

mccowan

Field Summary

Fields

Modifier and Type	Field and Description
static int	ILLUMINA_ALLEGED_MINIMUM_QUALITY

Constructor Summary

Constructors

Constructor and Description
BclQualityEvaluationStrategy(int minimumRevisedQuality)

Method Summary

Modifier and Type	Method and Description
void	assertMinimumQualities() Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
java.util.Map<java.lang.Byte,java.lang.Integer>	getPoorQualityFrequencies() Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
byte	reviseAndConditionallyLogQuality(byte quality) Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.

Methods inherited from class java.lang.Object

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

Field Detail

ILLUMINA_ALLEGED_MINIMUM_QUALITY

public static final int ILLUMINA_ALLEGED_MINIMUM_QUALITY

See Also:

Constant Field Values

Constructor Detail

BclQualityEvaluationStrategy

public BclQualityEvaluationStrategy(int minimumRevisedQuality)

Parameters:

minimumRevisedQuality - The minimum quality that should be seen from revised qualities; controls whether or not an exception is thrown when calling assertMinimumQualities()

Method Detail

reviseAndConditionallyLogQuality

public byte reviseAndConditionallyLogQuality(byte quality)

Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low. Because of (2) each record's quality should be passed only once to this method, otherwise it will be observed multiple times.

Parameters:

quality - The quality score read from the BCL

Returns:

The revised new quality score

assertMinimumQualities

public void assertMinimumQualities()

Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.

getPoorQualityFrequencies

public java.util.Map<java.lang.Byte,java.lang.Integer> getPoorQualityFrequencies()

Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.