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

P

parseBarcodeFile(ArrayList<String>, File) - Method in class uk.ac.sanger.npg.picard.IndexDecoder

read and check input bar code file

parseBarcodeString(ArrayList<String>, List<String>) - Method in class uk.ac.sanger.npg.picard.IndexDecoder

check the list of input bar codes.

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

The percentage of all reads in the lane that matched to this barcode.

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

The number of all reads matching this barcode that matched with 0 errors or no-calls.

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

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

The "normalized" matches to each barcode.

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

The number of PF reads matching this barcode that matched with 1 error or no-call.

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

The percentage of PF reads in the lane that matched to this barcode.

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

The number of PF reads matching this barcode that matched with 0 errors or no-calls.

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

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

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

The number of PF reads matching this barcode (always less than or equal to READS).

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

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

This is the base class for any command line program class

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

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

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

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

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

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

This class tries to open a Illumina position file including clocs, locs or pos file into a data input stream

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

PositionFileReader.Position - Class in uk.ac.sanger.npg.illumina.file.reader

position class

PositionFileReader.Position(String, String) - Constructor for class uk.ac.sanger.npg.illumina.file.reader.PositionFileReader.Position

prepareDecode(ArrayList<String>) - Method in class uk.ac.sanger.npg.picard.IndexDecoder

check input bar codes and initial bar codes object and metrics list

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

read each cluster and write them to output bam file

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

write BCL file to output stream tile by tile