htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>
, Closeable
, AutoCloseable
, Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
ClocsFileReader
, LocsFileReader
, PosFileReader
public abstract class AbstractIlluminaPositionFileReader extends Object implements htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractIlluminaPositionFileReader.PositionInfo |
Modifier and Type | Field | Description |
---|---|---|
static float |
MAX_POS |
|
static float |
MIN_POS |
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small
negative values and see what happens.
|
Constructor | Description |
---|---|
AbstractIlluminaPositionFileReader(File file) |
|
AbstractIlluminaPositionFileReader(File file,
int lane,
int tile) |
Use this ctor if lane and tile are not discernible from file name.
|
Modifier and Type | Method | Description |
---|---|---|
File |
getFile() |
|
int |
getLane() |
|
int |
getTile() |
|
abstract boolean |
hasNext() |
Return true if the file has more elements to return, false otherwise
|
protected abstract String |
makeExceptionMsg() |
Create a string that will be included in any NoSuchElementException thrown by the next() method
|
AbstractIlluminaPositionFileReader.PositionInfo |
next() |
Return the next set of coordinates in a given file.
|
void |
remove() |
|
protected abstract AbstractIlluminaPositionFileReader.PositionInfo |
unsafeNextInfo() |
Returns the next position info.
|
forEachRemaining
public static final float MAX_POS
public static final float MIN_POS
public AbstractIlluminaPositionFileReader(File file)
public AbstractIlluminaPositionFileReader(File file, int lane, int tile)
file
- lane
- tile
- public int getTile()
public int getLane()
public File getFile()
public final AbstractIlluminaPositionFileReader.PositionInfo next()
next
in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
protected abstract AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()
protected abstract String makeExceptionMsg()
public abstract boolean hasNext()
hasNext
in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
public void remove()
remove
in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>