PerTileFileUtil (picard 2.8.1 API)

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

public class PerTileFileUtil
extends ParameterizedFileUtil

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 and Description
`PerTileFileUtil(String extension, File base, FileFaker faker, int lane)`
`PerTileFileUtil(String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`List<String>`	`fakeFiles(List<Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format)` Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
`boolean`	`filesAvailable()` Determine whether or not files are available
`picard.illumina.parser.IlluminaFileMap`	`getFiles()`
`picard.illumina.parser.IlluminaFileMap`	`getFiles(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 picard.illumina.parser.ParameterizedFileUtil
fileToTile, getTiledFiles, getTiles, makeLaneTileRegex

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

- Constructor Detail
  - PerTileFileUtil
```
public PerTileFileUtil(String extension,
                       File base,
                       FileFaker faker,
                       int lane)
```
  - PerTileFileUtil
```
public PerTileFileUtil(String extension,
                       File base,
                       FileFaker faker,
                       int lane,
                       boolean skipEmptyFiles)
```
- Method Detail
  - filesAvailable
```
public boolean filesAvailable()
```
    Description copied from class: ParameterizedFileUtil
    
    Determine whether or not files are available
    
    Specified by:
    
    filesAvailable in class ParameterizedFileUtil
    
    Returns:
    
    return true if files are found matching this types pattern, false otherwise
  - getFiles
```
public picard.illumina.parser.IlluminaFileMap getFiles()
```
  - getFiles
```
public picard.illumina.parser.IlluminaFileMap getFiles(List<Integer> tiles)
```
  - 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
    
    Specified by:
    
    verify in class ParameterizedFileUtil
    
    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
  - fakeFiles
```
public List<String> fakeFiles(List<Integer> expectedTiles,
                              int[] cycles,
                              IlluminaFileUtil.SupportedIlluminaFormat format)
```
    Description copied from class: ParameterizedFileUtil
    
    Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
    
    Specified by:
    
    fakeFiles in class ParameterizedFileUtil
    
    Parameters:
    
    expectedTiles - An ordered list of tile numbers
    
    cycles - An ordered list of cycle numbers that may contain gaps
    
    format - The format of the files that are to be faked
    
    Returns:
    
    A list of error messages for this format

Class PerTileFileUtil

Field Summary

Fields inherited from class picard.illumina.parser.ParameterizedFileUtil

Constructor Summary

Method Summary

Methods inherited from class picard.illumina.parser.ParameterizedFileUtil

Methods inherited from class java.lang.Object

Constructor Detail

PerTileFileUtil

PerTileFileUtil

Method Detail

filesAvailable

getFiles

getFiles

verify

fakeFiles