htsjdk.samtools.fastq

Class FastqReader

java.lang.Object

htsjdk.samtools.fastq.FastqReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<FastqRecord>, java.util.Iterator<FastqRecord>

public class FastqReader
extends java.lang.Object
implements java.util.Iterator<FastqRecord>, java.lang.Iterable<FastqRecord>, java.io.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.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	FastqReader.LineType Enum of the types of lines we see in Fastq.

Constructor Summary

Constructors

Constructor and Description
FastqReader(java.io.BufferedReader reader)
FastqReader(java.io.File file)
FastqReader(java.io.File file, boolean skipBlankLines) Constructor
FastqReader(java.io.File file, java.io.BufferedReader reader)
FastqReader(java.io.File file, java.io.BufferedReader reader, boolean skipBlankLines) Constructor

Method Summary

Modifier and Type	Method and Description
protected void	checkLine(java.lang.String line, FastqReader.LineType kind) Checks that the line is neither null (representing EOF) or empty (blank line in file).
void	close()
protected java.lang.String	error(java.lang.String msg) Generates an error message with line number information.
java.io.File	getFile()
int	getLineNumber()
boolean	hasNext()
java.util.Iterator<FastqRecord>	iterator() WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not start iteration from the beginning of the file.
FastqRecord	next()
void	remove()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Iterator

forEachRemaining

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

FastqReader

public FastqReader(java.io.File file)

FastqReader

public FastqReader(java.io.File file,
                   boolean skipBlankLines)

Constructor

Parameters:

file - of FASTQ to read read. Will be opened with htsjdk.samtools.util.IOUtil.openFileForBufferedReading

skipBlankLines - should we skip blank lines ?

FastqReader

public FastqReader(java.io.BufferedReader reader)

FastqReader

public FastqReader(java.io.File file,
                   java.io.BufferedReader reader,
                   boolean skipBlankLines)

Constructor

Parameters:

file - Name of FASTQ being read, or null if not known.

reader - input reader . Will be closed by the close method

skipBlankLines - should we skip blank lines ?

FastqReader

public FastqReader(java.io.File file,
                   java.io.BufferedReader reader)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<FastqRecord>

next

public FastqRecord next()

Specified by:

next in interface java.util.Iterator<FastqRecord>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<FastqRecord>

iterator

public java.util.Iterator<FastqRecord> 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 interface java.lang.Iterable<FastqRecord>

getLineNumber

public int getLineNumber()

getFile

public java.io.File getFile()

Returns:

Name of FASTQ being read, or null if not known.

close

public void close()

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

checkLine

protected void checkLine(java.lang.String line,
                         FastqReader.LineType kind)

Checks that the line is neither null (representing EOF) or empty (blank line in file).

error

protected java.lang.String error(java.lang.String msg)

Generates an error message with line number information.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object