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

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main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.BCLFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.CLocsFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.FilterFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.LocsFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.PosFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.file.reader.SCLFileReader

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.Illumina2bam

main(String[]) - Static method in class uk.ac.sanger.npg.illumina.Tile

test main method

main(String[]) - Static method in class uk.ac.sanger.npg.picard.AlignmentFilter

main(String[]) - Static method in class uk.ac.sanger.npg.picard.BamIndexDecoder

main(String[]) - Static method in class uk.ac.sanger.npg.picard.BamMerger

example: ALIGNED=testdata/bam/6210_8_aligned.sam I=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_merged.bam TMP_DIR=testdata VALIDATION_STRINGENCY=SILENT

main(String[]) - Static method in class uk.ac.sanger.npg.picard.BamQualityQuantisation

main(String[]) - Static method in class uk.ac.sanger.npg.picard.BamReadTrimmer

example: INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT INPUT=testdata/bam/6210_8.sam OUTPUT=testdata/6210_8_trimmed.bam FIRST_POSITION_TO_TRIM=1 TRIM_LENGTH=3 TMP_DIR=testdata CREATE_MD5_FILE=true ONLY_FORWARD_READ=true SAVE_TRIM=true TRIM_BASE_TAG=rs TRIM_QUALITY_TAG=qs VALIDATION_STRINGENCY=SILENT

main(String[]) - Static method in class uk.ac.sanger.npg.picard.BamTagStripper

main(String[]) - Static method in class uk.ac.sanger.npg.picard.ChangeBamHeader

main(String[]) - Static method in class uk.ac.sanger.npg.picard.SplitBamByReadGroup

makeUniqueProgramId(List<SAMProgramRecord>, SAMProgramRecord) - Method in class uk.ac.sanger.npg.picard.PicardCommandLine

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

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

mergeRecords(SAMRecord, SAMRecord) - Method in class uk.ac.sanger.npg.picard.BamMerger

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

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

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