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

O

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

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

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

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

open all BCL or SCL files

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

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

log information

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

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

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

OUTPUT - Variable in class uk.ac.sanger.npg.picard.BamQualityQuantisation

output sam or bam file

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

OUTPUT - Variable in class uk.ac.sanger.npg.picard.BamTagStripper

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

OUTPUT_ALIGNMENT - Variable in class uk.ac.sanger.npg.picard.AlignmentFilter

OUTPUT_COMMON_RG_HEAD_TO_TRIM - Variable in class uk.ac.sanger.npg.picard.SplitBamByReadGroup

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

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

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

OUTPUT_PREFIX - Variable in class uk.ac.sanger.npg.picard.SplitBamByReadGroup

OUTPUT_UNALIGNED - Variable in class uk.ac.sanger.npg.picard.AlignmentFilter