public class ClippingUtility
extends java.lang.Object
Modifier and Type | Field and Description |
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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 and Description |
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ClippingUtility() |
Modifier and Type | Method and Description |
---|---|
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 java.lang.String |
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 |
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 |
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 |
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)
Deprecated.
Use the varargs version. This no longer returns a warning string..
|
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..
|
static AdapterPair |
adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
int minMatchBases,
double maxErrorRate,
AdapterPair... adapters)
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
|
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.
|
public static final int MIN_MATCH_BASES
public static final int MIN_MATCH_PE_BASES
public static final double MAX_ERROR_RATE
public static final double MAX_PE_ERROR_RATE
public static final int NO_MATCH
public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter)
public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter, int minMatchBases, double maxErrorRate)
public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters)
read
- SAM/BAM read to trimadapters
- which adapters to try to use (indexed, paired_end, or single_end)public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
read
- SAM/BAM read to trimminMatchBases
- minimum number of contiguous bases to match against in a readmaxErrorRate
- maximum error rate when matching read basesadapters
- which adapters to try (indexed, paired_end, or single_end)public static java.lang.String adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters)
public static java.lang.String adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters, int minMatchBases, double maxErrorRate)
public static AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters)
read1
- first read of the pairread2
- second read of the pairadapters
- which adapters to use (indexed, paired_end, or single_end, nextera), attempted in orderpublic static AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
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 complementedminMatchBases
- minimum number of contiguous bases to match against in a readmaxErrorRate
- maximum error rate when matching read basesadapters
- which adapters to use (indexed, paired_end, or single_end, nextera), attempted in orderpublic static int findIndexOfClipSequence(byte[] read, byte[] adapterSequence, int minMatch, double maxErrorRate)
read
-