picard.arrays.illumina

Class IlluminaAdpcFileWriter

java.lang.Object

picard.arrays.illumina.IlluminaAdpcFileWriter

All Implemented Interfaces:

java.lang.AutoCloseable

public class IlluminaAdpcFileWriter
extends java.lang.Object
implements java.lang.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)
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IlluminaAdpcFileWriter.Record

Constructor Summary

Constructors

Constructor and Description
IlluminaAdpcFileWriter(java.io.File adpcFile)

Method Summary

Modifier and Type	Method and Description
void	close()
void	write(java.lang.Iterable<IlluminaAdpcFileWriter.Record> illuminaAdpcRecords)

Methods inherited from class java.lang.Object

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

Constructor Detail

IlluminaAdpcFileWriter

public IlluminaAdpcFileWriter(java.io.File adpcFile)
                       throws java.io.IOException

Throws:

java.io.IOException

Method Detail

write

public void write(java.lang.Iterable<IlluminaAdpcFileWriter.Record> illuminaAdpcRecords)
           throws java.io.IOException

Throws:

java.io.IOException

close

public void close()
           throws java.lang.Exception

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.lang.Exception