picard.illumina.parser

Class PerTileFileUtil

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(java.lang.String extension, java.io.File base, FileFaker faker, int lane)
PerTileFileUtil(java.lang.String extension, java.io.File base, FileFaker faker, int lane, boolean skipEmptyFiles)

Method Summary

Modifier and Type	Method and Description
java.util.List<java.lang.String>	fakeFiles(java.util.List<java.lang.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(java.util.List<java.lang.Integer> tiles)
java.util.List<java.lang.String>	verify(java.util.List<java.lang.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(java.lang.String extension,
                       java.io.File base,
                       FileFaker faker,
                       int lane)

PerTileFileUtil

public PerTileFileUtil(java.lang.String extension,
                       java.io.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(java.util.List<java.lang.Integer> tiles)

verify

public java.util.List<java.lang.String> verify(java.util.List<java.lang.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 java.util.List<java.lang.String> fakeFiles(java.util.List<java.lang.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