picard.illumina.parser

Class PerTilePerCycleFileUtil

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

Method Summary

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.Set<java.lang.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(java.util.List<java.lang.Integer> tiles)
picard.illumina.parser.CycleIlluminaFileMap	getFiles(java.util.List<java.lang.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
java.util.List<java.lang.Integer>	getTiles() Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
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, makeLaneTileRegex

Methods inherited from class java.lang.Object

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

Constructor Detail

PerTilePerCycleFileUtil

public PerTilePerCycleFileUtil(java.lang.String extension,
                               java.io.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(java.util.List<java.lang.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(java.util.List<java.lang.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 java.util.Set<java.lang.Integer> getDetectedCycles()

getTiles

public java.util.List<java.lang.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 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[] 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