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

C

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

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

checkBarcodeQuality(String, String) - Method in class uk.ac.sanger.npg.picard.BamIndexDecoder

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

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

checkNextReadsForChimera(List<SAMRecord>, List<SAMRecord>) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

checkOneRecord(List<SAMRecord>, List<SAMRecord>, boolean) - Method in class uk.ac.sanger.npg.picard.AlignmentFilter

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

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

This class is a reader of a clocs file

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

Constructor

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

close file input stream

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

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

close all BCL or SCL file in not closed yet

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

close output files

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

convertByteArrayToString(byte[]) - Static method in class uk.ac.sanger.npg.bam.util.BamUtils

convertByteArrayToString(byte[]) - Method in class uk.ac.sanger.npg.illumina.Tile

convertPhredQualByteArrayToFastqString(byte[]) - Static method in class uk.ac.sanger.npg.bam.util.BamUtils

convertPhredQualByteArrayToFastqString(byte[]) - Method in class uk.ac.sanger.npg.illumina.Tile

currentTotalClusters - Variable in class uk.ac.sanger.npg.illumina.file.reader.PositionFileReader

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