Package picard.illumina.parser.readers

Class BclReader

  • All Implemented Interfaces:
    htsjdk.samtools.util.CloseableIterator<BclData>, Closeable, AutoCloseable, Iterator<BclData>
    public class BclReader
extends BaseBclReader
implements htsjdk.samtools.util.CloseableIterator<BclData>
    BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters. The file is structured as followed: Bytes 1-4 : unsigned int numClusters Bytes 5-numClusters + 5 : 1 byte base/quality score

    The base/quality scores are organized as follows (with one exception, SEE BELOW): The right 2 most bits (these are the LEAST significant bits) indicate the base, where A=00(0x00), C=01(0x01), G=10(0x02), and T=11(0x03)

    The remaining bytes compose the quality score which is an unsigned int.

    EXCEPTION: If a byte is entirely 0 (e.g. byteRead == 0) then it is a no call, the base becomes '.' and the Quality becomes 2, the default illumina masking value

    (E.g. if we get a value in binary of 10001011 it gets transformed as follows:

    Value read: 10001011(0x8B)

    Quality Base

    100010 11 00100010 0x03 0x22 T 34 T

    So the output base/quality will be a (T/34)