public class FastqReader extends java.lang.Object implements java.util.Iterator<FastqRecord>, java.lang.Iterable<FastqRecord>, java.io.Closeable
Constructor and Description |
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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
|
Modifier and Type | Method and Description |
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void |
close() |
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() |
public FastqReader(java.io.File file)
public FastqReader(java.io.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(java.io.BufferedReader reader)
public FastqReader(java.io.File file, java.io.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(java.io.File file, java.io.BufferedReader reader)
public boolean hasNext()
hasNext
in interface java.util.Iterator<FastqRecord>
public FastqRecord next()
next
in interface java.util.Iterator<FastqRecord>
public void remove()
remove
in interface java.util.Iterator<FastqRecord>
public java.util.Iterator<FastqRecord> iterator()
iterator
in interface java.lang.Iterable<FastqRecord>
public int getLineNumber()
public java.io.File getFile()
public void close()
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable
public java.lang.String toString()
toString
in class java.lang.Object