public class PileupIterator.Pileup
Inner class that captures pileup state at a specific position
| Modifiers | Name | Description |
|---|---|---|
int |
position |
| Type Params | Return Type | Name and description |
|---|---|---|
|
public int |
countOf(java.lang.String baseString) |
|
public int |
countOf(byte base) |
|
public int |
countOf(groovy.lang.Closure<java.lang.Object> c) |
|
public java.util.List<PileupState> |
getAlignments() |
|
public int[] |
getSummary()Returns a summary of the coverage at the location: |
|
public java.util.Map<java.lang.String, java.lang.Integer> |
getSummaryAsMap()Convenience method to return counts of each base as a map indexed by the base as a string. |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Returns a summary of the coverage at the location: [ A, T , C, G, Deletion, total ]
Convenience method to return counts of each base as a map indexed by the base as a string. This is not efficient, but useful in non performance sensitive contexts.