Package picard.analysis
Class AdapterUtility
- java.lang.Object
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- picard.analysis.AdapterUtility
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public class AdapterUtility extends 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).
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Field Summary
Fields Modifier and Type Field Description static List<String>
DEFAULT_ADAPTER_SEQUENCE
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Constructor Summary
Constructors Constructor Description AdapterUtility(List<String> adapterSequence)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
isAdapter(htsjdk.samtools.SAMRecord record)
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.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.boolean
isAdapterSequence(byte[] read, boolean revCompRead)
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.
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Method Detail
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isAdapter
public boolean isAdapter(htsjdk.samtools.SAMRecord record)
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.Only unmapped reads and reads with MQ=0 are considers eligible for being adapter
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isAdapterSequence
public boolean isAdapterSequence(byte[] read, boolean revCompRead)
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 themrevCompRead
- When aligned reads are checked for being adapter, this specified if the original read had ben rev-comped during alignment.- Returns:
- true if the read matches an adapter and false otherwise
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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
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