Package picard.illumina.parser.readers

Class BclReader

java.lang.Object
picard.illumina.parser.readers.BaseBclReader
picard.illumina.parser.readers.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)

  • Constructor Details

  • Method Details

    • isGzipped

      public static boolean isGzipped(File file)

    • isBlockGzipped

      public static boolean isBlockGzipped(File file)

    • getNumberOfClusters

      public static long getNumberOfClusters(File file)

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface htsjdk.samtools.util.CloseableIterator<BclData>

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<BclData>

    • assertProperFileStructure

      protected void assertProperFileStructure(File file)

    • next

      public BclData next()
      Specified by:
      next in interface Iterator<BclData>

    • remove

      public void remove()
      Specified by:
      remove in interface Iterator<BclData>

    • makeSeekable

      public static BclReader makeSeekable(List<File> files, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, int[] outputLengths)

    • seek

      public int seek(List<File> files, TileIndex tileIndex, int currentTile)