Package htsjdk.samtools.fastq
Class FastqReader
java.lang.Object
htsjdk.samtools.fastq.FastqReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,Iterable<FastqRecord>
,Iterator<FastqRecord>
public class FastqReader
extends Object
implements Iterator<FastqRecord>, Iterable<FastqRecord>, Closeable
Reads a FASTQ file with four lines per record.
WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not
start iteration from the beginning of the file. Developers should probably not call iterator()
directly. It is provided so that this class can be used in Java for-each loop.
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Nested Class Summary
Modifier and TypeClassDescriptionprotected static enum
Enum of the types of lines we see in Fastq. -
Constructor Summary
ConstructorDescriptionFastqReader
(BufferedReader reader) FastqReader
(File file) FastqReader
(File file, boolean skipBlankLines) ConstructorFastqReader
(File file, BufferedReader reader) FastqReader
(File file, BufferedReader reader, boolean skipBlankLines) Constructor -
Method Summary
Modifier and TypeMethodDescriptionprotected void
checkLine
(String line, FastqReader.LineType kind) Checks that the line is neither null (representing EOF) or empty (blank line in file).void
close()
protected String
Generates an error message with line number information.getFile()
int
boolean
hasNext()
iterator()
WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not start iteration from the beginning of the file.next()
void
remove()
toString()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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FastqReader
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FastqReader
Constructor- Parameters:
file
- of FASTQ to read read. Will be opened with htsjdk.samtools.util.IOUtil.openFileForBufferedReadingskipBlankLines
- should we skip blank lines ?
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FastqReader
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FastqReader
Constructor- Parameters:
file
- Name of FASTQ being read, or null if not known.reader
- input reader . Will be closed by the close methodskipBlankLines
- should we skip blank lines ?
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FastqReader
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Method Details
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hasNext
public boolean hasNext()- Specified by:
hasNext
in interfaceIterator<FastqRecord>
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next
- Specified by:
next
in interfaceIterator<FastqRecord>
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remove
public void remove()- Specified by:
remove
in interfaceIterator<FastqRecord>
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iterator
WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not start iteration from the beginning of the file. Developers should probably not call iterator() directly. It is provided so that this class can be used in Java for-each loop.- Specified by:
iterator
in interfaceIterable<FastqRecord>
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getLineNumber
public int getLineNumber() -
getFile
- Returns:
- Name of FASTQ being read, or null if not known.
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close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
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checkLine
Checks that the line is neither null (representing EOF) or empty (blank line in file). -
error
Generates an error message with line number information. -
toString
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