Package org.biojava.nbio.genome.io.fastq
Class SolexaFastqReader
- java.lang.Object
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- org.biojava.nbio.genome.io.fastq.SolexaFastqReader
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- All Implemented Interfaces:
FastqReader
public final class SolexaFastqReader extends Object
Reader forFastqVariant.FASTQ_SOLEXA
formatted sequences.- Since:
- 3.0.3
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Constructor Summary
Constructors Constructor Description SolexaFastqReader()
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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.void
parse(Readable readable, ParseListener listener)
Parse the specified readable.Iterable<Fastq>
read(File file)
Read zero or more FASTQ formatted sequences from the specified file.Iterable<Fastq>
read(InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream.Iterable<Fastq>
read(URL url)
Read zero or more FASTQ formatted sequences from the specified url.void
stream(Readable readable, StreamListener listener)
Stream the specified readable.
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Constructor Detail
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SolexaFastqReader
public SolexaFastqReader()
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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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parse
public final void parse(Readable readable, ParseListener listener) throws IOException
Description copied from interface:FastqReader
Parse the specified readable.- Specified by:
parse
in interfaceFastqReader
- Parameters:
readable
- readable, must not be nulllistener
- low-level event based parser callback, must not be null- Throws:
IOException
- if an I/O error occurs
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stream
public final void stream(Readable readable, StreamListener listener) throws IOException
Description copied from interface:FastqReader
Stream the specified readable.- Specified by:
stream
in interfaceFastqReader
- Parameters:
readable
- readable, must not be nulllistener
- event based reader callback, must not be null- Throws:
IOException
- if an I/O error occurs
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read
public final Iterable<Fastq> read(File file) throws IOException
Description copied from interface:FastqReader
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:
IOException
- if an I/O error occurs
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read
public final Iterable<Fastq> read(URL url) throws IOException
Description copied from interface:FastqReader
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:
IOException
- if an I/O error occurs
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read
public final Iterable<Fastq> read(InputStream inputStream) throws IOException
Description copied from interface:FastqReader
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:
IOException
- if an I/O error occurs
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