Uses of Interface
picard.util.AdapterPair

Packages that use AdapterPair

Package	Description
picard.util

Uses of AdapterPair in picard.util

Classes in picard.util that implement AdapterPair

Modifier and Type	Class and Description
static class	IlluminaUtil.IlluminaAdapterPair Describes adapters used on each pair of strands

Methods in picard.util that return AdapterPair

Modifier and Type	Method and Description
AdapterPair	AdapterMarker.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)
static AdapterPair	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters) Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
AdapterPair	AdapterMarker.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate) Overrides defaults for minMatchBases and maxErrorRate
static AdapterPair	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate, AdapterPair... adapters) Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
AdapterPair	AdapterMarker.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read)
static AdapterPair	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters) Invokes adapterTrimIlluminRead with default parameters for a single read.
AdapterPair	AdapterMarker.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate) Overrides defaults for minMatchBases and maxErrorRate
static AdapterPair	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters) Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.

Methods in picard.util with parameters of type AdapterPair

Modifier and Type	Method and Description
static AdapterPair	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters) Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
static java.lang.String	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters) Deprecated. Use the varargs version. This no longer returns a warning string..
static java.lang.String	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters, int minMatchBases, double maxErrorRate) Deprecated. Use the varargs version. This no longer returns a warning string..
static AdapterPair	ClippingUtility.adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate, AdapterPair... adapters) Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
static AdapterPair	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters) Invokes adapterTrimIlluminRead with default parameters for a single read.
static void	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter) Deprecated. Use the varargs version. This no longer returns a warning string..
static void	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter, int minMatchBases, double maxErrorRate) Deprecated. Use the varargs version. This no longer returns a warning string..
static AdapterPair	ClippingUtility.adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters) Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.

Constructors in picard.util with parameters of type AdapterPair

Constructor and Description
AdapterMarker(AdapterPair... originalAdapters) Truncates adapters to DEFAULT_ADAPTER_LENGTH
AdapterMarker(int adapterLength, AdapterPair... originalAdapters)