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

public class MultiTileBclFileUtil
extends ParameterizedFileUtil

NextSeq-style bcl's have all tiles for a cycle in a single file.

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`List<String>`	`fakeFiles(List<Integer> expectedTiles, int[] expectedCycles, 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.CycleIlluminaFileMap`	`getFiles(List<Integer> tiles, int[] cycles)`
`List<Integer>`	`getTiles()`	Return a list of all tiles available for this file format and run
`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
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile

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

- Method Detail
  - getFiles
```
public picard.illumina.parser.CycleIlluminaFileMap getFiles(List<Integer> tiles,
                                                            int[] cycles)
```
  - 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
  - getTiles
```
public List<Integer> getTiles()
```
    Description copied from class: ParameterizedFileUtil
    
    Return a list of all tiles available for this file format and run
    
    Overrides:
    
    getTiles in class ParameterizedFileUtil
    
    Returns:
    
    A List of tile integers
  - 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[] expectedCycles,
                              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
    
    expectedCycles - 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 MultiTileBclFileUtil

Field Summary

Fields inherited from class picard.illumina.parser.ParameterizedFileUtil

Method Summary

Methods inherited from class picard.illumina.parser.ParameterizedFileUtil

Methods inherited from class java.lang.Object

Method Detail

getFiles

filesAvailable

getTiles

verify

fakeFiles