| Class | Description |
|---|---|
| picard.fingerprint.CrosscheckReadGroupFingerprints |
6/6/2017 Use
CrosscheckFingerprints instead. |
| picard.sam.SetNmAndUqTags |
| Field | Description |
|---|---|
| picard.illumina.CheckIlluminaDirectory.LINK_LOCS |
It is no longer necessary to create locs file symlinks.
|
| picard.illumina.IlluminaBasecallsToFastq.ADAPTERS_TO_CHECK | |
| picard.sam.FastqToSam.STRIP_UNPAIRED_MATE_NUMBER | |
| picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED | |
| picard.sam.MergeBamAlignment.JUMP_SIZE | |
| picard.sam.MergeBamAlignment.PAIRED_RUN |
| Method | Description |
|---|---|
| picard.sam.CreateSequenceDictionary.makeSequenceDictionary(File) | |
| 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[]) |