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 and 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 and Description |
|---|
ErrorSummaryMetrics() |
| Modifier and Type | Method and Description |
|---|---|
void |
calculateDerivedFields()
placeholder method that will calculate the derived fields from the other ones.
|
canMerge, merge, merge, mergeIfCanpublic 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()
MergeableMetricBasecalculateDerivedFields in class MergeableMetricBase