Package picard.illumina.parser
Class IlluminaFileUtil
java.lang.Object
picard.illumina.parser.IlluminaFileUtil
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
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionIlluminaFileUtil
(File basecallDir, int lane) IlluminaFileUtil
(File basecallDir, File barcodeDir, int lane) -
Method Summary
Modifier and TypeMethodDescriptionGet the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the formatReturn 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 inspectingGiven a file type, get the Parameterized File Util object associated with itstatic boolean
static String
longLaneStr
(int lane)
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Field Details
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CYCLE_SUBDIRECTORY_PATTERN
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Constructor Details
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IlluminaFileUtil
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IlluminaFileUtil
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Method Details
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getLane
public int getLane()Return the lane we're inspecting -
getUtil
Given a file type, get the Parameterized File Util object associated with it -
getExpectedTiles
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin -
getActualTiles
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 -
tileMetricsOut
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longLaneStr
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hasCbcls
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