Package picard.illumina.parser
Class IlluminaFileUtil
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- picard.illumina.parser.IlluminaFileUtil
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public class IlluminaFileUtil extends Object
General utils for dealing with IlluminaFiles as well as utils for specific, support formats. This class contains utils that span across multiple Illumina files but it's primary intent was to provide support for basic file types. Each supported file type can be accessed via a factory method (makeFt). When IlluminaFileUtil is created it is parameterized by basecallDir and lane and all IlluminaFileTypes created by IlluminaFileUtil will also be parameterized in this fashion.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
IlluminaFileUtil.SupportedIlluminaFormat
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Field Summary
Fields Modifier and Type Field Description static Pattern
CYCLE_SUBDIRECTORY_PATTERN
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Constructor Summary
Constructors Constructor Description IlluminaFileUtil(File basecallDir, int lane)
IlluminaFileUtil(File basecallDir, File barcodeDir, int lane)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description List<Integer>
getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat> formats)
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the formatList<Integer>
getExpectedTiles()
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.binint
getLane()
Return the lane we're inspectingParameterizedFileUtil
getUtil(IlluminaFileUtil.SupportedIlluminaFormat format)
Given a file type, get the Parameterized File Util object associated with itstatic boolean
hasCbcls(File basecallDir, int lane)
static String
longLaneStr(int lane)
File
tileMetricsOut()
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Field Detail
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CYCLE_SUBDIRECTORY_PATTERN
public static final Pattern CYCLE_SUBDIRECTORY_PATTERN
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Method Detail
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getLane
public int getLane()
Return the lane we're inspecting
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getUtil
public ParameterizedFileUtil getUtil(IlluminaFileUtil.SupportedIlluminaFormat format)
Given a file type, get the Parameterized File Util object associated with it
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getExpectedTiles
public List<Integer> getExpectedTiles()
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
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getActualTiles
public List<Integer> getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat> formats)
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
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tileMetricsOut
public File tileMetricsOut()
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longLaneStr
public static String longLaneStr(int lane)
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hasCbcls
public static boolean hasCbcls(File basecallDir, int lane)
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