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Classes Class Description picard.fingerprint.CrosscheckReadGroupFingerprints 6/6/2017 UseCrosscheckFingerprints
instead.picard.sam.SetNmAndUqTags
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Fields Field Description picard.illumina.CheckIlluminaDirectory.LINK_LOCS It is no longer necessary to create locs file symlinks.picard.illumina.IlluminaBasecallsToFastq.ADAPTERS_TO_CHECK picard.sam.FastqToSam.STRIP_UNPAIRED_MATE_NUMBER picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED picard.sam.MergeBamAlignment.JUMP_SIZE picard.sam.MergeBamAlignment.PAIRED_RUN
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Methods Method Description picard.illumina.parser.TileMetricsUtil.parseTileMetrics(File, Map<Integer, File>, ReadStructure, ValidationStringency) picard.illumina.parser.TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(File, int, boolean) picard.sam.CreateSequenceDictionary.makeSequenceDictionary(File) picard.sam.DuplicationMetrics.calculateDerivedMetrics() picard.util.ClippingUtility.adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) Use the varargs version. This no longer returns a warning string..picard.util.ClippingUtility.adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) Use the varargs version. This no longer returns a warning string..picard.util.MathUtil.logLikelihoodsToProbs(double[])