Package picard.analysis.directed
Class TargetMetricsCollector.Coverage
- java.lang.Object
-
- picard.analysis.directed.TargetMetricsCollector.Coverage
-
- Enclosing class:
- TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
public static class TargetMetricsCollector.Coverage extends Object
A simple class that is used to store the coverage information about an interval.
-
-
Field Summary
Fields Modifier and Type Field Description long
readCount
-
Constructor Summary
Constructors Constructor Description Coverage(htsjdk.samtools.util.Interval i, int padding)
Constructs a new coverage object for the provided mapping with the desired padding either side.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addBase(int offset)
Adds a single point of depth at the desired offset into the coverage array.void
addBase(int offset, int depth)
Adds some depth at the desired offset into the coverage array.int[]
getDepths()
Gets the coverage depths as an array of ints.long
getTotal()
boolean
hasCoverage()
Returns true if any base in the range has coverage of > 0void
incrementReadCount()
Increments the # of reads mapping to this target.String
toString()
-
-
-
Method Detail
-
addBase
public void addBase(int offset)
Adds a single point of depth at the desired offset into the coverage array.
-
addBase
public void addBase(int offset, int depth)
Adds some depth at the desired offset into the coverage array.
-
incrementReadCount
public void incrementReadCount()
Increments the # of reads mapping to this target.
-
hasCoverage
public boolean hasCoverage()
Returns true if any base in the range has coverage of > 0
-
getDepths
public int[] getDepths()
Gets the coverage depths as an array of ints.
-
getTotal
public long getTotal()
-
-