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java.lang.Objectorg.biojava3.sequencing.io.fastq.SolexaFastqReader
public final class SolexaFastqReader
Reader for FastqVariant.FASTQ_SOLEXA
formatted sequences.
Constructor Summary | |
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SolexaFastqReader()
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Method Summary | ||
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protected FastqVariant |
getVariant()
Return the FASTQ sequence format variant for this reader. |
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parse(
Parse the specified input supplier. |
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Iterable<Fastq> |
read(File file)
Read zero or more FASTQ formatted sequences from the specified file. |
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Iterable<Fastq> |
read(InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream. |
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Iterable<Fastq> |
read(URL url)
Read zero or more FASTQ formatted sequences from the specified url. |
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stream(
Stream the specified input supplier. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SolexaFastqReader()
Method Detail |
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protected FastqVariant getVariant()
public final <R extends Readable & Closeable> void parse(supplier, ParseListener listener) throws IOException
parse
in interface FastqReader
supplier
- input supplier, must not be nulllistener
- low-level event based parser callback, must not be null
IOException
- if an I/O error occurspublic final <R extends Readable & Closeable> void stream(supplier, StreamListener listener) throws IOException
stream
in interface FastqReader
supplier
- input supplier, must not be nulllistener
- event based reader callback, must not be null
IOException
- if an I/O error occurspublic final Iterable<Fastq> read(File file) throws IOException
read
in interface FastqReader
file
- file to read from, must not be null
IOException
- if an I/O error occurspublic final Iterable<Fastq> read(URL url) throws IOException
read
in interface FastqReader
url
- URL to read from, must not be null
IOException
- if an I/O error occurspublic final Iterable<Fastq> read(InputStream inputStream) throws IOException
read
in interface FastqReader
inputStream
- input stream to read from, must not be null
IOException
- if an I/O error occurs
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