ClippingUtility (picard 2.18.2 API)

java.lang.Object
- picard.util.ClippingUtility

```
public class ClippingUtility
extends Object
```
Utilities to clip the adapter sequence from a SAMRecord read

Field Summary

Fields
Modifier and Type	Field	Description
`static double`	`MAX_ERROR_RATE`	The default value used for the maximum error rate when matching read bases to clippable sequence.
`static double`	`MAX_PE_ERROR_RATE`	The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
`static int`	`MIN_MATCH_BASES`	The default value used for the minimum number of contiguous bases to match against.
`static int`	`MIN_MATCH_PE_BASES`	The default value used for the minimum number of contiguous bases to match against in a paired end read
`static int`	`NO_MATCH`	The value returned by methods returning int when no match is found.

Constructor Summary

Constructors
Constructor Description

ClippingUtility()

Constructors
Constructor	Description
`ClippingUtility()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`static AdapterPair`	`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 String`	`adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters)`	Deprecated. Use the varargs version.
`static AdapterPair`	`adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters)`	Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
`static String`	`adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters, int minMatchBases, double maxErrorRate)`	Deprecated. Use the varargs version.
`static AdapterPair`	`adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters)`	Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
`static void`	`adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter)`	Deprecated. Use the varargs version.
`static AdapterPair`	`adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters)`	Invokes adapterTrimIlluminRead with default parameters for a single read.
`static void`	`adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter, int minMatchBases, double maxErrorRate)`	Deprecated. Use the varargs version.
`static int`	`findIndexOfClipSequence(byte[] read, byte[] adapterSequence, int minMatch, double maxErrorRate)`	Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MIN_MATCH_BASES
```
public static final int MIN_MATCH_BASES
```
    The default value used for the minimum number of contiguous bases to match against.
    
    See Also:
    
    Constant Field Values
  - MIN_MATCH_PE_BASES
```
public static final int MIN_MATCH_PE_BASES
```
    The default value used for the minimum number of contiguous bases to match against in a paired end read
    
    See Also:
    
    Constant Field Values
  - MAX_ERROR_RATE
```
public static final double MAX_ERROR_RATE
```
    The default value used for the maximum error rate when matching read bases to clippable sequence.
    
    See Also:
    
    Constant Field Values
  - MAX_PE_ERROR_RATE
```
public static final double MAX_PE_ERROR_RATE
```
    The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
    
    See Also:
    
    Constant Field Values
  - NO_MATCH
```
public static final int NO_MATCH
```
    The value returned by methods returning int when no match is found.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - ClippingUtility
```
public ClippingUtility()
```
- Method Detail
  - adapterTrimIlluminaSingleRead
```
public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
                                                 AdapterPair adapter)
```
    Deprecated.
    Use the varargs version. This no longer returns a warning string..
  - adapterTrimIlluminaSingleRead
```
public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
                                                 AdapterPair adapter,
                                                 int minMatchBases,
                                                 double maxErrorRate)
```
    Deprecated.
    Use the varargs version. This no longer returns a warning string..
  - adapterTrimIlluminaSingleRead
```
public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
                                                        AdapterPair... adapters)
```
    Invokes adapterTrimIlluminRead with default parameters for a single read. If the read is a negative strand, its bases will be reverse complemented Simpler, more common of two overloads. Accepts multiple adapters and tries them all until it finds the first one that matches.
    
    Parameters:
    
    read - SAM/BAM read to trim
    
    adapters - which adapters to try to use (indexed, paired_end, or single_end)
    
    Returns:
    
    AdapterPair the AdapterPair matched, or null
  - adapterTrimIlluminaSingleRead
```
public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
                                                        int minMatchBases,
                                                        double maxErrorRate,
                                                        AdapterPair... adapters)
```
    Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read. If the read is a negative strand, a copy of its bases will be reverse complemented. More general form of the two overloads. Accepts multiple adapters and tries them all until it finds the first one that matches.
    
    Parameters:
    
    read - SAM/BAM read to trim
    
    minMatchBases - minimum number of contiguous bases to match against in a read
    
    maxErrorRate - maximum error rate when matching read bases
    
    adapters - which adapters to try (indexed, paired_end, or single_end)
    
    Returns:
    
    AdapterPair the AdapterPair matched, or null
  - adapterTrimIlluminaPairedReads
```
public static String adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1,
                                                    htsjdk.samtools.SAMRecord read2,
                                                    AdapterPair adapters)
```
    Deprecated.
    Use the varargs version. This no longer returns a warning string..
  - adapterTrimIlluminaPairedReads
```
public static String 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..
  - adapterTrimIlluminaPairedReads
```
public static AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1,
                                                         htsjdk.samtools.SAMRecord read2,
                                                         AdapterPair... adapters)
```
    Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads. If the read is a negative strand, its bases will be reverse complemented Simpler, more common of two overloads.
    
    Parameters:
    
    read1 - first read of the pair
    
    read2 - second read of the pair
    
    adapters - which adapters to use (indexed, paired_end, or single_end, nextera), attempted in order
    
    Returns:
    
    int number of bases trimmed
  - adapterTrimIlluminaPairedReads
```
public static AdapterPair 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. More general form of two overloads. Returns a warning string when the trim positions found differed for each read.
    
    Parameters:
    
    read1 - first read of the pair. If read1 is a negative strand, a copy of its bases will be reverse complemented.
    
    read2 - second read of the pair. If read2 is a negative strand, a copy of its bases will be reverse complemented
    
    minMatchBases - minimum number of contiguous bases to match against in a read
    
    maxErrorRate - maximum error rate when matching read bases
    
    adapters - which adapters to use (indexed, paired_end, or single_end, nextera), attempted in order
    
    Returns:
    
    int number of bases trimmed
  - findIndexOfClipSequence
```
public static int findIndexOfClipSequence(byte[] read,
                                          byte[] adapterSequence,
                                          int minMatch,
                                          double maxErrorRate)
```
    Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
    
    Parameters:
    
    read -

Class ClippingUtility

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MIN_MATCH_BASES

MIN_MATCH_PE_BASES

MAX_ERROR_RATE

MAX_PE_ERROR_RATE

NO_MATCH

Constructor Detail

ClippingUtility

Method Detail

adapterTrimIlluminaSingleRead

adapterTrimIlluminaSingleRead

adapterTrimIlluminaSingleRead

adapterTrimIlluminaSingleRead

adapterTrimIlluminaPairedReads

adapterTrimIlluminaPairedReads

adapterTrimIlluminaPairedReads

adapterTrimIlluminaPairedReads

findIndexOfClipSequence