public final class IlluminaFastqReader
extends java.lang.Object
FastqVariant.FASTQ_ILLUMINA
formatted sequences.Constructor and Description |
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IlluminaFastqReader() |
Modifier and Type | Method and Description |
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protected FastqVariant |
getVariant()
Return the FASTQ sequence format variant for this reader.
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<R extends java.lang.Readable & java.io.Closeable> |
parse(
Parse the specified input supplier.
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java.lang.Iterable<Fastq> |
read(java.io.File file)
Read zero or more FASTQ formatted sequences from the specified file.
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java.lang.Iterable<Fastq> |
read(java.io.InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream.
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java.lang.Iterable<Fastq> |
read(java.net.URL url)
Read zero or more FASTQ formatted sequences from the specified url.
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<R extends java.lang.Readable & java.io.Closeable> |
stream(
Stream the specified input supplier.
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protected FastqVariant getVariant()
public final <R extends java.lang.Readable & java.io.Closeable> void parse(supplier, ParseListener listener) throws java.io.IOException
FastqReader
parse
in interface FastqReader
supplier
- input supplier, must not be nulllistener
- low-level event based parser callback, must not be nulljava.io.IOException
- if an I/O error occurspublic final <R extends java.lang.Readable & java.io.Closeable> void stream(supplier, StreamListener listener) throws java.io.IOException
FastqReader
stream
in interface FastqReader
supplier
- input supplier, must not be nulllistener
- event based reader callback, must not be nulljava.io.IOException
- if an I/O error occurspublic final java.lang.Iterable<Fastq> read(java.io.File file) throws java.io.IOException
FastqReader
read
in interface FastqReader
file
- file to read from, must not be nulljava.io.IOException
- if an I/O error occurspublic final java.lang.Iterable<Fastq> read(java.net.URL url) throws java.io.IOException
FastqReader
read
in interface FastqReader
url
- URL to read from, must not be nulljava.io.IOException
- if an I/O error occurspublic final java.lang.Iterable<Fastq> read(java.io.InputStream inputStream) throws java.io.IOException
FastqReader
read
in interface FastqReader
inputStream
- input stream to read from, must not be nulljava.io.IOException
- if an I/O error occurs