picard.illumina.parser

Class ParameterizedFileUtil

java.lang.Object

picard.illumina.parser.ParameterizedFileUtil

Direct Known Subclasses:

MultiTileBclFileUtil, MultiTileFileUtil, PerTileFileUtil, PerTilePerCycleFileUtil

public abstract class ParameterizedFileUtil
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected java.io.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 java.lang.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 java.util.regex.Pattern	matchPattern A pattern that will match files of this type for this lane
static java.lang.String	PER_TILE_PATTERN_STRING
protected boolean	skipEmptyFiles
protected java.util.List<java.lang.Integer>	tiles

Constructor Summary

Constructors

Constructor and Description
ParameterizedFileUtil(boolean laneTileRegex, java.lang.String extension, java.io.File base, FileFaker faker, int lane)
ParameterizedFileUtil(boolean laneTileRegex, java.lang.String extension, java.io.File base, FileFaker faker, int lane, boolean skipEmptyFiles)
ParameterizedFileUtil(java.lang.String pattern, java.lang.String extension, java.io.File base, FileFaker faker, int lane)

Method Summary

Modifier and Type	Method and Description
abstract 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.
abstract boolean	filesAvailable() Determine whether or not files are available
protected java.lang.Integer	fileToTile(java.lang.String fileName) Returns only lane and tile information as PerTileFt's do not have End information.
protected picard.illumina.parser.IlluminaFileMap	getTiledFiles(java.io.File baseDirectory, java.util.regex.Pattern pattern) Return all files that match pattern of the given file type in the given base directory
java.util.List<java.lang.Integer>	getTiles() Return a list of all tiles available for this file format and run
static java.lang.String	makeLaneTileRegex(java.lang.String fileNameEndPattern, int lane) Return a regex string for finding Lane and Tile given a file extension pattern
abstract 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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PER_TILE_PATTERN_STRING

public static final java.lang.String PER_TILE_PATTERN_STRING

See Also:

Constant Field Values

extension

protected final java.lang.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 java.util.regex.Pattern matchPattern

A pattern that will match files of this type for this lane

lane

protected final int lane

tiles

protected java.util.List<java.lang.Integer> tiles

base

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

ParameterizedFileUtil

public ParameterizedFileUtil(boolean laneTileRegex,
                             java.lang.String extension,
                             java.io.File base,
                             FileFaker faker,
                             int lane)

ParameterizedFileUtil

public ParameterizedFileUtil(java.lang.String pattern,
                             java.lang.String extension,
                             java.io.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 java.util.List<java.lang.Integer> getTiles()

Return a list of all tiles available for this file format and run

Returns:

A List of tile integers

verify

public abstract 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

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 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.

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 java.lang.Integer fileToTile(java.lang.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 java.lang.String makeLaneTileRegex(java.lang.String fileNameEndPattern,
                                                 int lane)

Return a regex string for finding Lane and Tile given a file extension pattern

getTiledFiles

protected picard.illumina.parser.IlluminaFileMap getTiledFiles(java.io.File baseDirectory,
                                                               java.util.regex.Pattern pattern)

Return all files that match pattern of the given file type in the given base directory