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

S

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

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

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

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

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

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

This class is a reader of a scl file

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

constructor to generate scl file input stream, and read the number of clusters and read all bases to an array

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

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

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

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

setChimericReadsCount(int[][]) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

setCycleRangeByRead(HashMap<String, int[]>) - Method in class uk.ac.sanger.npg.illumina.Lane

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

setIllumina2bamProgram(SAMProgramRecord) - Method in class uk.ac.sanger.npg.illumina.Lane

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

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

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

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

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

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

setReadsCountByAlignedNumForward(int[]) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

setReadsCountByAlignedNumReverse(int[]) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

setReadsCountPerRef(int[]) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

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

setRefList(ArrayList<ArrayList<AlignmentFilterMetric.SQ>>) - Method in class uk.ac.sanger.npg.picard.AlignmentFilterMetric

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

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

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

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

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

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

setTileList(int[]) - Method in class uk.ac.sanger.npg.illumina.Lane

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

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

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

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

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