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Classes Class Description picard.fastq.BamToBfqWriter 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.MAX_READS_IN_RAM_PER_TILE 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.fingerprint.FingerprintChecker.fingerprintSamFile(Path, IntervalList) 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[]) picard.util.SingleBarcodeDistanceMetric.leniantHammingDistance()
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Enum Constants Enum Constant Description picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.INDEL_EXTENSION_ERROR - but used in existing extended manifest files.picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.INDEL_SEQ_MISMATCH - but used in existing extended manifest files.picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.PROBE_SEQUENCE_STRAND_INVALID - but used in existing extended manifest files.picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.SEQUENCE_MISMATCH - but used in existing extended manifest files.picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.SOURCE_SEQUENCE_MISMATCH - but used in existing extended manifest files.picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag.SOURCE_SEQUENCE_STRAND_INVALID - but used in existing extended manifest files.