A B C D E F G H I K L M N O P Q R S T U V W X Y

B

BamIndexDecoder - Class in uk.ac.sanger.npg.picard

This class is used decode the multiplexed bam file.

BamIndexDecoder() - Constructor for class uk.ac.sanger.npg.picard.BamIndexDecoder

BamMerger - Class in uk.ac.sanger.npg.picard

A command-line tool to merge BAM/SAM alignment info in a bam with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM.

BamMerger() - Constructor for class uk.ac.sanger.npg.picard.BamMerger

BamQualityQuantisation - Class in uk.ac.sanger.npg.picard

BamQualityQuantisation() - Constructor for class uk.ac.sanger.npg.picard.BamQualityQuantisation

BamReadTrimmer - Class in uk.ac.sanger.npg.picard

The class to strip part of a read (fixed position) - typically a prefix of the forward read, and optionally place this and its quality in BAM tags.

BamReadTrimmer() - Constructor for class uk.ac.sanger.npg.picard.BamReadTrimmer

BamTagStripper - Class in uk.ac.sanger.npg.picard

BamTagStripper() - Constructor for class uk.ac.sanger.npg.picard.BamTagStripper

BamUtils - Class in uk.ac.sanger.npg.bam.util

illumina2bam bam util class

BamUtils() - Constructor for class uk.ac.sanger.npg.bam.util.BamUtils

BARCODE - Variable in class uk.ac.sanger.npg.picard.BamIndexDecoder

BARCODE - Variable in class uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMetric

The barcode (from the set of expected barcodes) for which the following metrics apply.

barcode - Variable in class uk.ac.sanger.npg.picard.IndexDecoder.NamedBarcode

BARCODE_FILE - Variable in class uk.ac.sanger.npg.picard.BamIndexDecoder

BARCODE_NAME - Variable in class uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMetric

BARCODE_QUALITY_TAG_NAME - Variable in class uk.ac.sanger.npg.illumina.Illumina2bam

BARCODE_QUALITY_TAG_NAME - Variable in class uk.ac.sanger.npg.picard.BamIndexDecoder

BARCODE_SEQUENCE_TAG_NAME - Variable in class uk.ac.sanger.npg.illumina.Illumina2bam

BARCODE_TAG_NAME - Variable in class uk.ac.sanger.npg.picard.BamIndexDecoder

barcodeBytes - Variable in class uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMetric

barcodeName - Variable in class uk.ac.sanger.npg.picard.IndexDecoder.NamedBarcode

BASECALLS_DIR - Variable in class uk.ac.sanger.npg.illumina.Illumina2bam

BCLFileReader - Class in uk.ac.sanger.npg.illumina.file.reader

This class is a reader of a bcl file

BCLFileReader(String) - Constructor for class uk.ac.sanger.npg.illumina.file.reader.BCLFileReader

constructor to generate bcl file input stream and read the number of clusters