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

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 picard.illumina.parser.PerTileFileUtil
fakeFiles, getFiles, getFiles

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

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

Constructor Details
- PerTileOrPerRunFileUtil
  
  public PerTileOrPerRunFileUtil(String extension, File base, FileFaker faker, int lane)
Method Details
- 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