@groovy.util.logging.Log class TargetedCoverageCalculator extends java.lang.Object
Optimised class to count reads over a given set of target regions
| Constructor and description |
|---|
TargetedCoverageCalculator
(SAM bam, Regions regions) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
void |
calculateChrCoverage(java.lang.String chr, int[] results, int startRegionIndex)Count the number of reads overlapping each target region from the given chromosome |
|
int[] |
countReads()Return an integer array containing the number of reads overlapping each of the intervals in the bam file. |
| 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() |
Count the number of reads overlapping each target region from the given chromosome
chr - chromosomeresults - results array, will be populated from startPosReturn an integer array containing the number of reads overlapping each of the intervals in the bam file. @return
Groovy Documentation