public class AdapterMarker
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_ADAPTER_LENGTH |
static int |
DEFAULT_NUM_ADAPTERS_TO_KEEP |
static int |
DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN |
Constructor and Description |
---|
AdapterMarker(AdapterPair... originalAdapters)
Truncates adapters to DEFAULT_ADAPTER_LENGTH
|
AdapterMarker(int adapterLength,
AdapterPair... originalAdapters) |
Modifier and Type | Method and Description |
---|---|
AdapterPair |
adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1,
htsjdk.samtools.SAMRecord read2) |
AdapterPair |
adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1,
htsjdk.samtools.SAMRecord read2,
int minMatchBases,
double maxErrorRate)
Overrides defaults for minMatchBases and maxErrorRate
|
AdapterPair |
adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read) |
AdapterPair |
adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read,
int minMatchBases,
double maxErrorRate)
Overrides defaults for minMatchBases and maxErrorRate
|
double |
getMaxPairErrorRate() |
double |
getMaxSingleEndErrorRate() |
int |
getMinPairMatchBases() |
int |
getMinSingleEndMatchBases() |
int |
getNumAdaptersToKeep() |
int |
getThresholdForSelectingAdaptersToKeep() |
AdapterMarker |
setMaxPairErrorRate(double maxPairErrorRate) |
AdapterMarker |
setMaxSingleEndErrorRate(double maxSingleEndErrorRate) |
AdapterMarker |
setMinPairMatchBases(int minPairMatchBases) |
AdapterMarker |
setMinSingleEndMatchBases(int minSingleEndMatchBases) |
AdapterMarker |
setNumAdaptersToKeep(int numAdaptersToKeep)
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
|
AdapterMarker |
setThresholdForSelectingAdaptersToKeep(int thresholdForSelectingAdaptersToKeep)
When this number of adapters have been matched, discard the least-frequently matching ones.
|
public static final int DEFAULT_ADAPTER_LENGTH
public static final int DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN
public static final int DEFAULT_NUM_ADAPTERS_TO_KEEP
public AdapterMarker(AdapterPair... originalAdapters)
originalAdapters
- These should be in order from longest & most likely to shortest & least likely.public AdapterMarker(int adapterLength, AdapterPair... originalAdapters)
adapterLength
- Truncate adapters to this length.originalAdapters
- These should be in order from longest & most likely to shortest & least likely.public int getNumAdaptersToKeep()
public AdapterMarker setNumAdaptersToKeep(int numAdaptersToKeep)
public int getThresholdForSelectingAdaptersToKeep()
public AdapterMarker setThresholdForSelectingAdaptersToKeep(int thresholdForSelectingAdaptersToKeep)
thresholdForSelectingAdaptersToKeep
- set to -1 to never discard any adapters.public int getMinSingleEndMatchBases()
public AdapterMarker setMinSingleEndMatchBases(int minSingleEndMatchBases)
minSingleEndMatchBases
- When marking a single-end read, adapter must match at least this many bases.public int getMinPairMatchBases()
public AdapterMarker setMinPairMatchBases(int minPairMatchBases)
minPairMatchBases
- When marking a paired-end read, adapter must match at least this many bases.public double getMaxSingleEndErrorRate()
public AdapterMarker setMaxSingleEndErrorRate(double maxSingleEndErrorRate)
maxSingleEndErrorRate
- For single-end read, no more than this fraction of the bases that align with the adapter can
mismatch the adapter and still be considered an adapter match.public double getMaxPairErrorRate()
public AdapterMarker setMaxPairErrorRate(double maxPairErrorRate)
maxPairErrorRate
- For paired-end read, no more than this fraction of the bases that align with the adapter can
mismatch the adapter and still be considered an adapter match.public AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read)
public AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)
public AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate)
public AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate)