PerTilePerCycleFileUtil (picard 2.8.1 API)

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

public class PerTilePerCycleFileUtil
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
`PerTilePerCycleFileUtil(String extension, File base, FileFaker faker, int lane)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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
`Set<Integer>`	`getDetectedCycles()`
`picard.illumina.parser.CycleIlluminaFileMap`	`getFiles()`
`picard.illumina.parser.CycleIlluminaFileMap`	`getFiles(int[] cycles)` Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
`picard.illumina.parser.CycleIlluminaFileMap`	`getFiles(List<Integer> tiles)`
`picard.illumina.parser.CycleIlluminaFileMap`	`getFiles(List<Integer> tiles, int[] cycles)` Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
`protected picard.illumina.parser.CycleIlluminaFileMap`	`getPerTilePerCycleFiles()` For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
`List<Integer>`	`getTiles()` Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
`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, makeLaneTileRegex

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

- Constructor Detail
  - PerTilePerCycleFileUtil
```
public PerTilePerCycleFileUtil(String extension,
                               File base,
                               FileFaker faker,
                               int lane)
```
- Method Detail
  - getPerTilePerCycleFiles
```
protected picard.illumina.parser.CycleIlluminaFileMap getPerTilePerCycleFiles()
```
    For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
    
    Returns:
    
    A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available cycles if expectedCycles is null)
  - getFiles
```
public picard.illumina.parser.CycleIlluminaFileMap getFiles()
```
  - getFiles
```
public picard.illumina.parser.CycleIlluminaFileMap getFiles(List<Integer> tiles)
```
  - getFiles
```
public picard.illumina.parser.CycleIlluminaFileMap getFiles(int[] cycles)
```
    Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing cycle files or directories will be removed from the cycle list that is kept.
    
    Parameters:
    
    cycles - Cycles that should be present in the output CycleIlluminaFileMap
    
    Returns:
    
    A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
  - getFiles
```
public picard.illumina.parser.CycleIlluminaFileMap getFiles(List<Integer> tiles,
                                                            int[] cycles)
```
    Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
    
    Parameters:
    
    cycles - Cycles that should be present in the output CycleIlluminaFileMap
    
    Returns:
    
    A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
  - getDetectedCycles
```
public Set<Integer> getDetectedCycles()
```
  - getTiles
```
public List<Integer> getTiles()
```
    Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files. The same number of tiles is expected in each cycle dir.
    
    Overrides:
    
    getTiles in class ParameterizedFileUtil
    
    Returns:
    
    A list of tile integers for all tiles available
  - 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
  - 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 PerTilePerCycleFileUtil

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

PerTilePerCycleFileUtil

Method Detail

getPerTilePerCycleFiles

getFiles

getFiles

getFiles

getFiles

getDetectedCycles

getTiles

filesAvailable

verify

fakeFiles