Package picard.arrays.illumina
Class IlluminaAdpcFileWriter
- java.lang.Object
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- picard.arrays.illumina.IlluminaAdpcFileWriter
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- All Implemented Interfaces:
AutoCloseable
public class IlluminaAdpcFileWriter extends Object implements AutoCloseable
A class to encompass writing an Illumina adpc.bin file.This file is used as input to verifyIDIntensity, a contamination checking tool for Illumina Genotyping Arrays.
Here is the format of the file
The file size is (16 byte offset) + (18 bytes) * # INDS * SNP
Note that I do not know what the header (16 bytes) should contain. verifyIDIntensity, does not care, so we are putting garbage in there now. I presume it *should* contain the number of probes (at a minimum)
Each genotype is ordered in the following way. (ind1-snp1) - (ind1-snp2) - (ind1-snp3) ... (ind1-snpN) (ind2-snp1)
The 18 bytes are composed of the following information.
2-short - A intensity 2-short - B intensity 4-float - A normalized intensity 4-float - B normalized intensity 4-float - GC score : clustering confidence 2-short - genotype value : 0 (AA) 1 (AB) 2 (BB) 3 (NN)
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
IlluminaAdpcFileWriter.Record
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Constructor Summary
Constructors Constructor Description IlluminaAdpcFileWriter(File adpcFile)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
void
write(Iterable<IlluminaAdpcFileWriter.Record> illuminaAdpcRecords)
void
write(IlluminaAdpcFileWriter.Record illuminaAdpcRecord)
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Constructor Detail
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IlluminaAdpcFileWriter
public IlluminaAdpcFileWriter(File adpcFile) throws IOException
- Throws:
IOException
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Method Detail
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write
public void write(Iterable<IlluminaAdpcFileWriter.Record> illuminaAdpcRecords) throws IOException
- Throws:
IOException
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write
public void write(IlluminaAdpcFileWriter.Record illuminaAdpcRecord) throws IOException
- Throws:
IOException
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close
public void close() throws Exception
- Specified by:
close
in interfaceAutoCloseable
- Throws:
Exception
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