public class ErrorSummaryMetrics extends MergeableMetricBase
CollectSequencingArtifactMetrics
as a roll up of the
context-specific error rates, to provide global error rates per type of base substitution.
Errors are normalized to the lexically lower reference base and summarized together. E.g.
G>T is converted to C>A and merged with data from C>A for reporting.MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
Modifier and Type | Field | Description |
---|---|---|
char |
ALT_BASE |
The alternative base (or it's complement).
|
long |
ALT_COUNT |
The number of alt bases observed.
|
char |
REF_BASE |
The reference base (or it's complement).
|
long |
REF_COUNT |
The number of reference bases observed.
|
String |
SUBSTITUTION |
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
|
double |
SUBSTITUTION_RATE |
The rate of the substitution in question.
|
Constructor | Description |
---|---|
ErrorSummaryMetrics() |
Modifier and Type | Method | Description |
---|---|---|
void |
calculateDerivedFields() |
placeholder method that will calculate the derived fields from the other ones.
|
canMerge, merge, merge, mergeIfCan
public char REF_BASE
public char ALT_BASE
public String SUBSTITUTION
public long REF_COUNT
public long ALT_COUNT
public double SUBSTITUTION_RATE
public void calculateDerivedFields()
MergeableMetricBase
calculateDerivedFields
in class MergeableMetricBase