Deprecated API

Contents

• Deprecated Fields
• Deprecated Methods

Deprecated Fields

Field and Description
picard.sam.MergeBamAlignment.PAIRED_RUN

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.util.MathUtil.logLikelihoodsToProbs(double[])