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

A

addProgramRecordToHead(SAMFileHeader, SAMProgramRecord) - Method in class uk.ac.sanger.npg.picard.PicardCommandLine

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

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

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

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

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

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

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

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

AlignmentFilterMetric.SQ - Class in uk.ac.sanger.npg.picard

SQ record in SAM header

AlignmentFilterMetric.SQ(String, String, String, int, String) - Constructor for class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ

AlignmentFilterMetric.SQ(SAMSequenceRecord) - Constructor for class uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ