Package picard.analysis.directed
Class TargetMetricsCollector.Coverage
java.lang.Object
picard.analysis.directed.TargetMetricsCollector.Coverage
- Enclosing class:
- TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
A simple class that is used to store the coverage information about an interval.
-
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionCoverage
(htsjdk.samtools.util.Interval i, int padding) Constructs a new coverage object for the provided mapping with the desired padding either side. -
Method Summary
Modifier and TypeMethodDescriptionvoid
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[]
Gets the coverage depths as an array of ints.long
getTotal()
boolean
Returns true if any base in the range has coverage of > 0void
Increments the # of reads mapping to this target.toString()
-
Field Details
-
readCount
public long readCount
-
-
Constructor Details
-
Coverage
public Coverage(htsjdk.samtools.util.Interval i, int padding) Constructs a new coverage object for the provided mapping with the desired padding either side.
-
-
Method Details
-
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() -
toString
-