FastqReader (htsjdk 2.14.3 API)

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.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

protected static class FastqReader.LineType
Enum of the types of lines we see in Fastq.

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

Constructor Summary

Constructors
Constructor	Description
`FastqReader(BufferedReader reader)`
`FastqReader(File file)`
`FastqReader(File file, boolean skipBlankLines)`	Constructor
`FastqReader(File file, BufferedReader reader)`
`FastqReader(File file, BufferedReader reader, boolean skipBlankLines)`	Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected 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`	`error(String msg)`	Generates an error message with line number information.
`File`	`getFile()`
`int`	`getLineNumber()`
`boolean`	`hasNext()`
`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()`
`String`	`toString()`

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - FastqReader
```
public FastqReader(File file)
```
  - FastqReader
```
public FastqReader(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(BufferedReader reader)
```
  - FastqReader
```
public FastqReader(File file,
                   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(File file,
                   BufferedReader reader)
```
- Method Detail
  - hasNext
```
public boolean hasNext()
```
    Specified by:
    
    hasNext in interface Iterator<FastqRecord>
  - next
```
public FastqRecord next()
```
    Specified by:
    
    next in interface Iterator<FastqRecord>
  - remove
```
public void remove()
```
    Specified by:
    
    remove in interface Iterator<FastqRecord>
  - iterator
```
public 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 Iterable<FastqRecord>
  - getLineNumber
```
public int getLineNumber()
```
  - getFile
```
public File getFile()
```
    Returns:
    
    Name of FASTQ being read, or null if not known.
  - close
```
public void close()
```
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
  - checkLine
```
protected void checkLine(String line,
                         FastqReader.LineType kind)
```
    Checks that the line is neither null (representing EOF) or empty (blank line in file).
  - error
```
protected String error(String msg)
```
    Generates an error message with line number information.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class FastqReader

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from interface java.lang.Iterable

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Constructor Detail

FastqReader

FastqReader

FastqReader

FastqReader

FastqReader

Method Detail

hasNext

next

remove

iterator

getLineNumber

getFile

close

checkLine

error

toString