Package uk.ac.sanger.npg.picard

Class Summary

AlignmentFilter
AlignmentFilterMetric
AlignmentFilterMetric.SQ	SQ record in SAM header
BamIndexDecoder	This class is used decode the multiplexed bam file.
BamMerger	A command-line tool to merge BAM/SAM alignment info in a bam with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM.
BamQualityQuantisation
BamReadTrimmer	The class to strip part of a read (fixed position) - typically a prefix of the forward read, and optionally place this and its quality in BAM tags.
BamTagStripper
ChangeBamHeader
IndexDecoder	This class was separated from Picard ExtractIlluminaBarcodes class, which originally only decode the reads in qseq files.
IndexDecoder.BarcodeMatch	BarcodeMatch class
IndexDecoder.BarcodeMetric	Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
IndexDecoder.NamedBarcode	Barcode Class
PicardCommandLine	This is the base class for any command line program class
SplitBamByReadGroup