| Class and Description |
|---|
| picard.analysis.directed.CalculateHsMetrics |
| picard.analysis.CollectWgsMetricsFromQuerySorted |
| picard.analysis.CollectWgsMetricsFromSampledSites |
| picard.fingerprint.GenotypeReader
Please use VCFFileReader instead of this class.
|
| Field and Description |
|---|
| picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED |
| picard.sam.MergeBamAlignment.PAIRED_RUN |
| 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.util.MathUtil.logLikelihoodsToProbs(double[]) |
| 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.
|