Package picard.arrays.illumina
Class IlluminaBPMFile
- java.lang.Object
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- picard.arrays.illumina.InfiniumDataFile
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- picard.arrays.illumina.IlluminaBPMFile
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- All Implemented Interfaces:
AutoCloseable
public class IlluminaBPMFile extends InfiniumDataFile implements AutoCloseable
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
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Field Summary
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Fields inherited from class picard.arrays.illumina.InfiniumDataFile
MAX_UNSIGNED_SHORT
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Constructor Summary
Constructors Constructor Description IlluminaBPMFile(File bpmFile)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
int[]
getAllNormalizationIds()
String
getControlConfig()
IlluminaBPMLocusEntry[]
getLocusEntries()
String
getManifestName()
Integer[]
getUniqueNormalizationIds()
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Methods inherited from class picard.arrays.illumina.InfiniumDataFile
byteArrayToCharArray, byteArrayToFloat, byteArrayToInt, floatToByteArray, getIdentifier, setIdentifier, shortToByteArray
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Constructor Detail
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IlluminaBPMFile
public IlluminaBPMFile(File bpmFile) throws IOException
- Throws:
IOException
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Method Detail
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close
public void close() throws IOException
- Specified by:
close
in interfaceAutoCloseable
- Throws:
IOException
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getManifestName
public String getManifestName()
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getControlConfig
public String getControlConfig()
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getLocusEntries
public IlluminaBPMLocusEntry[] getLocusEntries()
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getAllNormalizationIds
public int[] getAllNormalizationIds()
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getUniqueNormalizationIds
public Integer[] getUniqueNormalizationIds()
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