Deprecated List (picard 2.8.1 API)

Deprecated Classes
Class	Description
picard.analysis.directed.CalculateHsMetrics
picard.analysis.CollectWgsMetricsFromQuerySorted
picard.analysis.CollectWgsMetricsFromSampledSites
picard.fingerprint.GenotypeReader	Please use VCFFileReader instead of this class.
picard.sam.SetNmAndUqTags

Deprecated Fields
Field	Description
picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED
picard.sam.MergeBamAlignment.PAIRED_RUN
picard.sam.FastqToSam.STRIP_UNPAIRED_MATE_NUMBER

Deprecated Methods
Method	Description
picard.util.ClippingUtility.adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair)	Use the varargs version. This no longer returns a warning string..
picard.util.ClippingUtility.adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double)	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.ClippingUtility.adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double)	Use the varargs version. This no longer returns a warning string..
picard.sam.DuplicationMetrics.calculateDerivedMetrics()
picard.util.MathUtil.logLikelihoodsToProbs(double[])
picard.sam.CreateSequenceDictionary.makeSequenceDictionary(File)
picard.fingerprint.GenotypeReader.read(File)	Please use VCFFileReader in Picard-public instead of this class.
picard.fingerprint.GenotypeReader.read(File, IntervalList)	Please use VCFFileReader in Picard-public instead of this class.

Deprecated API