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java.lang.Objectorg.biojava3.sequencing.io.fastq.FastqTools
public final class FastqTools
Utility methods for FASTQ formatted sequences.
Method Summary | |
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static DNASequence |
createDNASequence(Fastq fastq)
Create and return a new DNASequence from the specified FASTQ formatted sequence. |
static DNASequence |
createDNASequenceWithErrorProbabilities(Fastq fastq)
Create and return a new DNASequence with error probabilities from the specified
FASTQ formatted sequence. |
static DNASequence |
createDNASequenceWithQualityScores(Fastq fastq)
Create and return a new DNASequence with quality scores from the specified
FASTQ formatted sequence. |
static DNASequence |
createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
Create and return a new DNASequence with quality scores and error probabilities from the
specified FASTQ formatted sequence. |
static QuantityFeature |
createErrorProbabilities(Fastq fastq)
Create and return a new QuantityFeature from the error probabilities of the specified
FASTQ formatted sequence. |
static QualityFeature |
createQualityScores(Fastq fastq)
Create and return a new QualityFeature from the quality scores of the specified
FASTQ formatted sequence. |
static Iterable<Double> |
errorProbabilities(Fastq fastq)
Return the error probabilities from the specified FASTQ formatted sequence. |
static double[] |
errorProbabilities(Fastq fastq,
double[] errorProbabilities)
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array. |
static Iterable<Integer> |
qualityScores(Fastq fastq)
Return the quality scores from the specified FASTQ formatted sequence. |
static int[] |
qualityScores(Fastq fastq,
int[] qualityScores)
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static DNASequence createDNASequence(Fastq fastq)
DNASequence
from the specified FASTQ formatted sequence.
fastq
- FASTQ formatted sequence, must not be null
DNASequence
from the specified FASTQ formatted sequencepublic static DNASequence createDNASequenceWithQualityScores(Fastq fastq)
DNASequence
with quality scores from the specified
FASTQ formatted sequence. The quality scores are stored in a QualityFeature
with a type "qualityScores"
the same length as the sequence.
fastq
- FASTQ formatted sequence, must not be null
DNASequence
with quality scores from the specified FASTQ formatted sequencepublic static DNASequence createDNASequenceWithErrorProbabilities(Fastq fastq)
DNASequence
with error probabilities from the specified
FASTQ formatted sequence. The error probabilities are stored in a QuantityFeature
with a type "errorProbabilities"
the same length as the sequence.
fastq
- FASTQ formatted sequence, must not be null
DNASequence
with error probabilities from the specified FASTQ formatted sequencepublic static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
DNASequence
with quality scores and error probabilities from the
specified FASTQ formatted sequence. The quality scores are stored in a QualityFeature
with a type "qualityScores"
the same length as the sequence and the error
probabilities are stored in a QuantityFeature
with a type "errorProbabilities"
the same length as the sequence.
fastq
- FASTQ formatted sequence, must not be null
DNASequence
with quality scores and error probabilities from the specified
FASTQ formatted sequencepublic static QualityFeature createQualityScores(Fastq fastq)
QualityFeature
from the quality scores of the specified
FASTQ formatted sequence. The quality scores feature has a type "qualityScores"
and will be the same length as the sequence.
fastq
- FASTQ formatted sequence, must not be null
QualityFeature
from the quality scores of the specified FASTQ
formatted sequencepublic static QuantityFeature createErrorProbabilities(Fastq fastq)
QuantityFeature
from the error probabilities of the specified
FASTQ formatted sequence. The error probabilities feature has a type "errorProbabilities"
and will be the same length as the sequence.
fastq
- FASTQ formatted sequence, must not be null
QualityFeature
from the error probabilities of the specified FASTQ
formatted sequencepublic static Iterable<Integer> qualityScores(Fastq fastq)
fastq
- FASTQ formatted sequence, must not be null
public static int[] qualityScores(Fastq fastq, int[] qualityScores)
fastq
- FASTQ formatted sequence, must not be nullqualityScores
- int array of quality scores, must not be null and must be the same
length as the FASTQ formatted sequence quality
public static Iterable<Double> errorProbabilities(Fastq fastq)
fastq
- FASTQ formatted sequence, must not be null
public static double[] errorProbabilities(Fastq fastq, double[] errorProbabilities)
fastq
- FASTQ formatted sequence, must not be nullerrorProbabilities
- double array of error probabilities, must not be null and must be the same
length as the FASTQ formatted sequence quality
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