Package org.biojava.bio.program.fastq
Class IlluminaFastqReader
- java.lang.Object
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- org.biojava.bio.program.fastq.IlluminaFastqReader
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- All Implemented Interfaces:
FastqReader
public final class IlluminaFastqReader extends java.lang.Object
Reader forFastqVariant.FASTQ_ILLUMINA
formatted sequences.
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Constructor Summary
Constructors Constructor Description IlluminaFastqReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected FastqVariant
getVariant()
Return the FASTQ sequence format variant for this reader.java.lang.Iterable<Fastq>
read(java.io.File file)
Read zero or more FASTQ formatted sequences from the specified file.java.lang.Iterable<Fastq>
read(java.io.InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream.java.lang.Iterable<Fastq>
read(java.net.URL url)
Read zero or more FASTQ formatted sequences from the specified url.protected void
validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber)
Validate the specified description.protected void
validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber)
Validate the specified quality scores.protected void
validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber)
Validate the specified repeat description.protected void
validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber)
Validate the specified sequence.
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Method Detail
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getVariant
protected FastqVariant getVariant()
Return the FASTQ sequence format variant for this reader.- Returns:
- the FASTQ sequence format variant for this reader
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validateDescription
protected void validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber) throws java.io.IOException
Validate the specified description.- Parameters:
builder
- FASTQ formatted sequence builder, will not be nulldescription
- description to validate, will not be nulllineNumber
- current line number in input stream- Throws:
java.io.IOException
- if the specified description is not valid
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validateSequence
protected void validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber) throws java.io.IOException
Validate the specified sequence.- Parameters:
builder
- FASTQ formatted sequence builder, will not be nullsequence
- sequence to validate, will not be nulllineNumber
- current line number in input stream- Throws:
java.io.IOException
- if the specified sequence is not valid
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validateRepeatDescription
protected void validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber) throws java.io.IOException
Validate the specified repeat description.- Parameters:
builder
- FASTQ formatted sequence builder, will not be nullrepeatDescription
- repeat description to validate, will not be nulllineNumber
- current line number in input stream- Throws:
java.io.IOException
- if the specified repeat description is not valid
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validateQuality
protected void validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber) throws java.io.IOException
Validate the specified quality scores.- Parameters:
builder
- FASTQ formatted sequence builder, will not be nullquality
- quality scores to validate, will not be nulllineNumber
- current line number in input stream- Throws:
java.io.IOException
- if the specified quality scores are not valid
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read
public final java.lang.Iterable<Fastq> read(java.io.File file) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified file.- Specified by:
read
in interfaceFastqReader
- Parameters:
file
- file to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified file
- Throws:
java.io.IOException
- if an IO error occurs
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read
public final java.lang.Iterable<Fastq> read(java.net.URL url) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified url.- Specified by:
read
in interfaceFastqReader
- Parameters:
url
- URL to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified url
- Throws:
java.io.IOException
- if an IO error occurs
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read
public final java.lang.Iterable<Fastq> read(java.io.InputStream inputStream) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified input stream.- Specified by:
read
in interfaceFastqReader
- Parameters:
inputStream
- input stream to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified input stream
- Throws:
java.io.IOException
- if an IO error occurs
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