Deprecated API

Contents

• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Enum Constants

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
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection.DEPRECATED_RecoverDanglingHeads
picard.sam.MergeBamAlignment.JUMP_SIZE
picard.illumina.CheckIlluminaDirectory.LINK_LOCS It is no longer necessary to create locs file symlinks.
org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.NO_CALL_ALLELES you should use GATKVariantContextUtils.noCallAlleles(int) instead. It indicates the presence of a hardcoded diploid assumption which is bad.
picard.sam.MergeBamAlignment.PAIRED_RUN
picard.sam.FastqToSam.STRIP_UNPAIRED_MATE_NUMBER
org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.tumorSample
org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection.useNewAFCalculator

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()
org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature.getChr()
org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getCodingSequence(ReferenceContext, List<? extends Locatable>, Strand)
picard.util.MathUtil.logLikelihoodsToProbs(double[])
picard.illumina.parser.TileMetricsUtil.parseTileMetrics(File, Map<Integer, File>, ReadStructure, ValidationStringency) use TileMetricsUtil.parseClusterRecordsFromTileMetricsV3(Collection, Map, ReadStructure) instead
picard.illumina.parser.TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(File, int, boolean) use TileMetricsUtil.findTileMetricsFiles(File, int, boolean) instead

Deprecated Enum Constants

Enum Constant and 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.SEQUENCE_MISMATCH - but used in existing extended manifest files.