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

G

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

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

generateOutputFile(SAMFileHeader) - Method in class uk.ac.sanger.npg.picard.BamIndexDecoder

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

generateSamReadGroupRecord(String, Date) - Method in class uk.ac.sanger.npg.illumina.Illumina2bam

Generate read group record

getAs() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ

getBarcodeLength() - Method in class uk.ac.sanger.npg.picard.IndexDecoder

getBaseCallFileName(int, boolean) - Method in class uk.ac.sanger.npg.illumina.Tile

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

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

getChimericReadsCount() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

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

getCurrentBlock() - Method in class uk.ac.sanger.npg.illumina.file.reader.CLocsFileReader

getCurrentCluster() - Method in class uk.ac.sanger.npg.illumina.file.reader.BCLFileReader

getCurrentCluster() - Method in class uk.ac.sanger.npg.illumina.file.reader.FilterFileReader

getCurrentCluster() - Method in class uk.ac.sanger.npg.illumina.file.reader.SCLFileReader

getCurrentPFClusters() - Method in class uk.ac.sanger.npg.illumina.file.reader.FilterFileReader

getCurrentTotalClusters() - Method in class uk.ac.sanger.npg.illumina.file.reader.PositionFileReader

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

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

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

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

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

getIllumina2bamProgram() - Method in class uk.ac.sanger.npg.illumina.Lane

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

getLn() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ

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

getNamedBarcodes() - Method in class uk.ac.sanger.npg.picard.IndexDecoder

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

read bases and qualities for next cluster of one read

getNextClusterBaseQuals(BCLFileReader[]) - Method in class uk.ac.sanger.npg.illumina.Tile

read bases and qualities for next cluster of one read from its BCL file list

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

read second bases for next cluster of one read

getNextClusterSecondBases(SCLFileReader[]) - Method in class uk.ac.sanger.npg.illumina.Tile

read second bases for next cluster of one read from its BCL file list

getNumberAlignments() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

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

getProgramRecordFromString(String) - Method in class uk.ac.sanger.npg.picard.ChangeBamHeader

getReadInfoFromRunParametersOrRunInfoFile(String, Document) - Method in class uk.ac.sanger.npg.illumina.Lane

From runParameters file: "RunParameters/Setup/Reads/Read" for HiSeq, "RunParameters/Reads/RunInfoRead" for MiSeq and no file for GA From RunInfo file: "RunInfo/Run/Reads/Read" only for HiSeq and MiSeq, not cope with GA

getReadName(String[]) - Method in class uk.ac.sanger.npg.illumina.Tile

form read name for one cluster

getReadsCountByAlignedNumForward() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

getReadsCountByAlignedNumReverse() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

getReadsCountPerRef() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

getReadsCountUnaligned() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

getRefList() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

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

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

getSAMRecord(SAMFileHeader, String, int, byte[][], String, byte[][], byte[][], int, boolean, boolean) - Method in class uk.ac.sanger.npg.illumina.Tile

write all together for one SAM Record

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

getSn() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ

getSp() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ

getThisProgramRecord(String, String) - Method in class uk.ac.sanger.npg.picard.PicardCommandLine

Generate Program Record for this program itself

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

getTotalBlocks() - Method in class uk.ac.sanger.npg.illumina.file.reader.CLocsFileReader

getTotalCluster() - Method in class uk.ac.sanger.npg.illumina.file.reader.LocsFileReader

getTotalCluster() - Method in class uk.ac.sanger.npg.illumina.file.reader.PosFileReader

getTotalClusters() - Method in class uk.ac.sanger.npg.illumina.file.reader.BCLFileReader

getTotalClusters() - Method in class uk.ac.sanger.npg.illumina.file.reader.FilterFileReader

getTotalClusters() - Method in class uk.ac.sanger.npg.illumina.file.reader.SCLFileReader

getTotalReads() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

getUr() - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ