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

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Illumina2bam - Class in uk.ac.sanger.npg.illumina

This is the main class to convert Illumina BCL files to BAM

Illumina2bam() - Constructor for class uk.ac.sanger.npg.illumina.Illumina2bam

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

This class tries to open a Illumina file into a data input stream.

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

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

This class was separated from Picard ExtractIlluminaBarcodes class, which originally only decode the reads in qseq files.

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

default constructor

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

Constructor from a file with bar code list

IndexDecoder(List<String>) - Constructor for class uk.ac.sanger.npg.picard.IndexDecoder

constructor from a list of barcodes

IndexDecoder.BarcodeMatch - Class in uk.ac.sanger.npg.picard

BarcodeMatch class

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

IndexDecoder.BarcodeMetric - Class in uk.ac.sanger.npg.picard

Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.

IndexDecoder.BarcodeMetric(IndexDecoder.NamedBarcode) - Constructor for class uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMetric

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

This ctor is necessary for when reading metrics from file

IndexDecoder.NamedBarcode - Class in uk.ac.sanger.npg.picard

Barcode Class

IndexDecoder.NamedBarcode(String, String, String, String, String) - Constructor for class uk.ac.sanger.npg.picard.IndexDecoder.NamedBarcode

IndexDecoder.NamedBarcode(String) - Constructor for class uk.ac.sanger.npg.picard.IndexDecoder.NamedBarcode

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

INPUT - Variable in class uk.ac.sanger.npg.picard.BamMerger

INPUT - Variable in class uk.ac.sanger.npg.picard.BamQualityQuantisation

input sam or bam file

INPUT - Variable in class uk.ac.sanger.npg.picard.BamReadTrimmer

INPUT - Variable in class uk.ac.sanger.npg.picard.BamTagStripper

INPUT - Variable in class uk.ac.sanger.npg.picard.ChangeBamHeader

INPUT - Variable in class uk.ac.sanger.npg.picard.SplitBamByReadGroup

INPUT_ALIGNMENT - Variable in class uk.ac.sanger.npg.picard.AlignmentFilter

inputStream - Variable in class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

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

isIndexed() - Method in class uk.ac.sanger.npg.illumina.Tile

isPairedRead() - Method in class uk.ac.sanger.npg.illumina.Tile