PerTileOrPerRunFileUtil (picard 2.18.2 API)

java.lang.Object
- picard.illumina.parser.ParameterizedFileUtil
- - picard.illumina.parser.PerTileFileUtil
  - - picard.illumina.parser.PerTileOrPerRunFileUtil

public class PerTileOrPerRunFileUtil
extends PerTileFileUtil

Field Summary
- Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
  base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles

Constructor Summary

Constructors
Constructor	Description
`PerTileOrPerRunFileUtil(String extension, File base, FileFaker faker, int lane)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`checkTileCount()`
`boolean`	`filesAvailable()`	Determine whether or not files are available
`void`	`setTilesForPerRunFile(List<Integer> tiles)`
`List<String>`	`verify(List<Integer> expectedTiles, int[] expectedCycles)`	Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files

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

Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
escapePeriods, fileToTile, getRunFile, getTiledFiles, getTiles, makeBarcodeRegex, makeLaneTileRegex, setTiles

Methods inherited from class picard.illumina.parser.PerTileFileUtil
fakeFiles, getFiles, getFiles

- Constructor Detail
  - PerTileOrPerRunFileUtil
```
public PerTileOrPerRunFileUtil(String extension,
                               File base,
                               FileFaker faker,
                               int lane)
```
- Method Detail
  - filesAvailable
```
public boolean filesAvailable()
```
    Description copied from class: ParameterizedFileUtil
    
    Determine whether or not files are available
    
    Overrides:
    
    filesAvailable in class PerTileFileUtil
    
    Returns:
    
    return true if files are found matching this types pattern, false otherwise
  - setTilesForPerRunFile
```
public void setTilesForPerRunFile(List<Integer> tiles)
```
    Overrides:
    
    setTilesForPerRunFile in class ParameterizedFileUtil
  - checkTileCount
```
public boolean checkTileCount()
```
    Overrides:
    
    checkTileCount in class ParameterizedFileUtil
  - verify
```
public List<String> verify(List<Integer> expectedTiles,
                           int[] expectedCycles)
```
    Description copied from class: ParameterizedFileUtil
    
    Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
    
    Overrides:
    
    verify in class PerTileFileUtil
    
    Parameters:
    
    expectedTiles - An ordered list of tile numbers
    
    expectedCycles - An ordered list of cycle numbers that may contain gaps
    
    Returns:
    
    A list of error messages for this format

Class PerTileOrPerRunFileUtil

Field Summary

Fields inherited from class picard.illumina.parser.ParameterizedFileUtil

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class picard.illumina.parser.ParameterizedFileUtil

Methods inherited from class picard.illumina.parser.PerTileFileUtil

Constructor Detail

PerTileOrPerRunFileUtil

Method Detail

filesAvailable

setTilesForPerRunFile

checkTileCount

verify