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

R

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

The rate of all reads matching this barcode to all reads matching the most prevelant barcode.

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

readBarCodeIndexCycles() - Method in class uk.ac.sanger.npg.illumina.Lane

readBaseCallProgramRecord() - Method in class uk.ac.sanger.npg.illumina.Lane

readConfigs() - Method in class uk.ac.sanger.npg.illumina.Lane

Read both config XML files under BaseCalls and Intensities.

readCycleRangeByRead() - Method in class uk.ac.sanger.npg.illumina.Lane

readFourBytes() - Method in class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

read four bytes from its input stream and convert to unsigned integer

readFourBytes(DataInputStream) - Method in class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

read four bytes from an input stream and convert to unsigned integer

readInstrumentAndRunID() - Method in class uk.ac.sanger.npg.illumina.Lane

readInstrumentProgramRecord() - Method in class uk.ac.sanger.npg.illumina.Lane

readInstrumentProgramRecordFromRunParameterFile() - Method in class uk.ac.sanger.npg.illumina.Lane

readRunDate() - Method in class uk.ac.sanger.npg.illumina.Lane

readRunfoder() - Method in class uk.ac.sanger.npg.illumina.Lane

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

The total number of reads matching the barcode.

readTileList() - Method in class uk.ac.sanger.npg.illumina.Lane

readTileRange() - Method in class uk.ac.sanger.npg.illumina.Lane

reduceTileList(Integer, Integer) - Method in class uk.ac.sanger.npg.illumina.Lane

remove() - Method in class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

removeAlignment(SAMRecord, SAMFileHeader) - Method in class uk.ac.sanger.npg.picard.BamReadTrimmer

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

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

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