Class IlluminaAdpcFileWriter

java.lang.Object
picard.arrays.illumina.IlluminaAdpcFileWriter
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)