Deprecated API

Contents

• Deprecated Classes
• Deprecated Fields
• Deprecated Methods

Deprecated Classes

Class and Description
picard.fingerprint.CrosscheckReadGroupFingerprints 6/6/2017 Use CrosscheckFingerprints instead.
picard.sam.SetNmAndUqTags

Deprecated Fields

Field and Description
picard.illumina.IlluminaBasecallsToFastq.ADAPTERS_TO_CHECK
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)