picard.analysis

Class AdapterUtility

java.lang.Object

picard.analysis.AdapterUtility

public class AdapterUtility
extends java.lang.Object

A utility class for matching reads to adapters. Note that this is different from ClippingUtility in that it tries to match the starts of reads to any part of the adapter (as opposed to finding the start of the adapter anywhere in the read).

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.List<java.lang.String>	DEFAULT_ADAPTER_SEQUENCE

Constructor Summary

Constructors

Constructor and Description
AdapterUtility(java.util.List<java.lang.String> adapterSequence)

Method Summary

Modifier and Type	Method and Description
boolean	isAdapterSequence(byte[] read) Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_ADAPTER_SEQUENCE

public static java.util.List<java.lang.String> DEFAULT_ADAPTER_SEQUENCE

Constructor Detail

AdapterUtility

public AdapterUtility(java.util.List<java.lang.String> adapterSequence)

Method Detail

isAdapterSequence

public boolean isAdapterSequence(byte[] read)

Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.

Parameters:

read - the basecalls for the read in the order and orientation the machine read them

Returns:

true if the read matches an adapter and false otherwise