picard.illumina.parser

Class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>

java.lang.Object

picard.illumina.parser.ParameterizedFileUtil

picard.illumina.parser.MultiTileFileUtil<OUTPUT_RECORD>

public abstract class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
extends ParameterizedFileUtil

For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.io.File	bci
protected java.io.File	dataFile
protected TileIndex	tileIndex

Fields inherited from class picard.illumina.parser.ParameterizedFileUtil

base, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, tiles

Method Summary

Methods

Modifier and Type	Method and Description
java.util.List<java.lang.String>	fakeFiles(java.util.List<java.lang.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
java.util.List<java.lang.Integer>	getTiles() Return a list of all tiles available for this file format and run
java.util.List<java.lang.String>	verify(java.util.List<java.lang.Integer> expectedTiles, int[] expectedCycles) expectedCycles are not checked in this implementation.

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

Field Detail

bci

protected final java.io.File bci

tileIndex

protected TileIndex tileIndex

dataFile

protected java.io.File dataFile

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

getTiles

public java.util.List<java.lang.Integer> getTiles()

Description copied from class: ParameterizedFileUtil

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

Overrides:

getTiles in class ParameterizedFileUtil

Returns:

A List of tile integers

verify

public java.util.List<java.lang.String> verify(java.util.List<java.lang.Integer> expectedTiles,
                                      int[] expectedCycles)

expectedCycles are not checked in this implementation.

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[] 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