ParameterizedFileUtil (picard 2.18.2 API)

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

Direct Known Subclasses:

MultiTileBclFileUtil, MultiTileFileUtil, PerTileFileUtil, PerTilePerCycleFileUtil
```
public abstract class ParameterizedFileUtil
extends Object
```

Field Summary

Fields
Modifier and Type	Field	Description
`protected File`	`base`	If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
`protected static boolean`	`DefaultSkipEmptyFiles`
`protected String`	`extension`	The file extension for this class, file extension does not have the standard meaning in this instance.
`protected FileFaker`	`faker`
`protected int`	`lane`
`protected Pattern`	`matchPattern`	A pattern that will match files of this type for this lane
`static String`	`PER_TILE_PATTERN_STRING`
`protected boolean`	`skipEmptyFiles`
`protected List<Integer>`	`tiles`

Constructor Summary

Constructors
Constructor	Description
`ParameterizedFileUtil(boolean laneTileRegex, String extension, File base, FileFaker faker, int lane)`
`ParameterizedFileUtil(boolean laneTileRegex, String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles)`
`ParameterizedFileUtil(String pattern, String extension, File base, FileFaker faker, int lane)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`checkTileCount()`
`static String`	`escapePeriods(String preEscaped)`	Escape the period character.
`abstract 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.
`abstract boolean`	`filesAvailable()`	Determine whether or not files are available
`protected Integer`	`fileToTile(String fileName)`	Returns only lane and tile information as PerTileFt's do not have End information.
`protected File`	`getRunFile(File baseDirectory, Pattern pattern)`
`protected picard.illumina.parser.IlluminaFileMap`	`getTiledFiles(File baseDirectory, Pattern pattern)`	Return all files that match pattern of the given file type in the given base directory
`List<Integer>`	`getTiles()`	Return a list of all tiles available for this file format and run
`static String`	`makeBarcodeRegex(int lane)`
`static String`	`makeLaneTileRegex(String fileNameEndPattern, int lane)`	Return a regex string for finding Lane and Tile given a file extension pattern
`void`	`setTiles(List<Integer> tiles)`
`void`	`setTilesForPerRunFile(List<Integer> tiles)`
`abstract 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

Field Detail
- PER_TILE_PATTERN_STRING
```
public static final String PER_TILE_PATTERN_STRING
```
  See Also:
  
  Constant Field Values
- extension
```
protected final String extension
```
  The file extension for this class, file extension does not have the standard meaning in this instance. It means, all the characters that come after the identifying portion of the file (after lane, tile, and end that is). So _qseq.txt and .filter are both file extensions
- matchPattern
```
protected Pattern matchPattern
```
  A pattern that will match files of this type for this lane
- lane
```
protected final int lane
```
- tiles
```
protected List<Integer> tiles
```
- base
```
protected final File base
```
  If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g. If we're talking about BCLs the directory structure is:
  BaseCall Dir | L001 | | | C1.1 C2.1 ... Cn.1 | | | bcl Files ... bclFiles
  L001 is the base because it contains every BCL file in the run (though those files are nested in other folders).
- faker
```
protected final FileFaker faker
```
- DefaultSkipEmptyFiles
```
protected static final boolean DefaultSkipEmptyFiles
```
  See Also:
  
  Constant Field Values
- skipEmptyFiles
```
protected final boolean skipEmptyFiles
```

Constructor Detail

ParameterizedFileUtil

public ParameterizedFileUtil(boolean laneTileRegex,
                             String extension,
                             File base,
                             FileFaker faker,
                             int lane,
                             boolean skipEmptyFiles)

ParameterizedFileUtil

public ParameterizedFileUtil(boolean laneTileRegex,
                             String extension,
                             File base,
                             FileFaker faker,
                             int lane)

ParameterizedFileUtil

public ParameterizedFileUtil(String pattern,
                             String extension,
                             File base,
                             FileFaker faker,
                             int lane)

Method Detail
- filesAvailable
```
public abstract boolean filesAvailable()
```
  Determine whether or not files are available
  
  Returns:
  
  return true if files are found matching this types pattern, false otherwise
- getTiles
```
public List<Integer> getTiles()
```
  Return a list of all tiles available for this file format and run
  
  Returns:
  
  A List of tile integers
- verify
```
public abstract 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
  
  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 abstract 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.
  
  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
- fileToTile
```
protected Integer fileToTile(String fileName)
```
  Returns only lane and tile information as PerTileFt's do not have End information.
  
  Parameters:
  
  fileName - Filename to analyze for data
  
  Returns:
  
  A LaneTile object with the discovered Lane and Tile information and a null end field.
- makeLaneTileRegex
```
public static String makeLaneTileRegex(String fileNameEndPattern,
                                       int lane)
```
  Return a regex string for finding Lane and Tile given a file extension pattern
- escapePeriods
```
public static String escapePeriods(String preEscaped)
```
  Escape the period character.
- getRunFile
```
protected File getRunFile(File baseDirectory,
                          Pattern pattern)
```
- getTiledFiles
```
protected picard.illumina.parser.IlluminaFileMap getTiledFiles(File baseDirectory,
                                                               Pattern pattern)
```
  Return all files that match pattern of the given file type in the given base directory
- setTiles
```
public void setTiles(List<Integer> tiles)
```
- setTilesForPerRunFile
```
public void setTilesForPerRunFile(List<Integer> tiles)
```
- checkTileCount
```
public boolean checkTileCount()
```
- makeBarcodeRegex
```
public static String makeBarcodeRegex(int lane)
```

Class ParameterizedFileUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PER_TILE_PATTERN_STRING

extension

matchPattern

lane

tiles

base

faker

DefaultSkipEmptyFiles

skipEmptyFiles

Constructor Detail

ParameterizedFileUtil

ParameterizedFileUtil

ParameterizedFileUtil

Method Detail

filesAvailable

getTiles

verify

fakeFiles

fileToTile

makeLaneTileRegex

escapePeriods

getRunFile

getTiledFiles

setTiles

setTilesForPerRunFile

checkTileCount

makeBarcodeRegex