Closeable
, AutoCloseable
, Iterable<FastqRecord>
, Iterator<FastqRecord>
public class FastqReader extends Object implements Iterator<FastqRecord>, Iterable<FastqRecord>, Closeable
Modifier and Type | Class | Description |
---|---|---|
protected static class |
FastqReader.LineType |
Enum of the types of lines we see in Fastq.
|
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
|
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() |
forEach, spliterator
forEachRemaining
public FastqReader(File file)
public FastqReader(File file, boolean skipBlankLines)
file
- of FASTQ to read read. Will be opened with htsjdk.samtools.util.IOUtil.openFileForBufferedReadingskipBlankLines
- should we skip blank lines ?public FastqReader(BufferedReader reader)
public FastqReader(File file, BufferedReader reader, boolean skipBlankLines)
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 ?public FastqReader(File file, BufferedReader reader)
public boolean hasNext()
hasNext
in interface Iterator<FastqRecord>
public FastqRecord next()
next
in interface Iterator<FastqRecord>
public void remove()
remove
in interface Iterator<FastqRecord>
public Iterator<FastqRecord> iterator()
iterator
in interface Iterable<FastqRecord>
public int getLineNumber()
public File getFile()
public void close()
close
in interface AutoCloseable
close
in interface Closeable
protected void checkLine(String line, FastqReader.LineType kind)