public class FastqReader extends Object implements Iterator<FastqRecord>, Iterable<FastqRecord>, Closeable
Constructor and Description |
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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
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Modifier and Type | Method and Description |
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void |
close() |
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() |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
forEachRemaining
forEach, spliterator
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 Closeable
close
in interface AutoCloseable