# Deprecated API

## Contents

- Deprecated Classes
- Deprecated Fields
- Deprecated Methods

- Deprecated Classes
  Class and 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 and Description
  picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED
  picard.sam.MergeBamAlignment.PAIRED_RUN
  picard.sam.FastqToSam.STRIP_UNPAIRED_MATE_NUMBER

- Deprecated Methods
  Method and 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.