VCFFilter
public class SampleMissing extends SampleFilter
Constructor | Description |
---|---|
SampleMissing(double threshold,
int minDepth) |
Constructor
|
SampleMissing(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Constructor from a config (read in from a XML file)
|
Modifier and Type | Method | Description |
---|---|---|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for this filter
|
java.lang.String |
getSummary() |
Gets a string summary of this filter
|
boolean |
test(Sample s) |
Tests whether a sample should be filtered out
|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
change
public SampleMissing(double threshold, int minDepth)
threshold
- The missing thresholdminDepth
- The minimum number of reads required for a genotype to
be considered presentpublic SampleMissing(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic boolean test(Sample s) throws VCFDataException
SampleFilter
test
in class SampleFilter
s
- The sample to testVCFDataException
- If there is a problem with the
data in the VCFpublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()
VCFFilter
public java.lang.String getSummary()
VCFFilter