MeanCoverageEstimator

Summary:
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Constructor
Method

| Detail:
Property
Constructor
Method

gngs.tools.MeanCoverageEstimator

```
@groovy.util.logging.Log
class MeanCoverageEstimator
extends java.lang.Object
```
Estimates the mean coverage of a BAM file quickly through random sampling.
Regions for sampling are selected randomly from a provided BED file. Sampling continues until either the standard deviation of the mean estimate (the mean of the sampled means) falls below a threshold, or until a maximum number of iterations occurs.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`SAM`	`bam`
`int`	`maxRegions`
`int`	`minRegions`
`int`	`padding`
`java.util.Random`	`random`
`Regions`	`regions`
`double`	`sdThreshold`
`boolean`	`verbose`

Constructor Summary

Constructors
Constructor and description
`MeanCoverageEstimator (SAM sam, Regions regions)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`double`	`estimate()`
	`java.util.List<Region>`	`generateRandomSamplingRegions()`
	`static void`	`main(java.lang.String[] args)`

Inherited Methods Summary

Inherited Methods
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()`

- Property Detail
  - SAM bam
  - int maxRegions
  - int minRegions
  - int padding
  - java.util.Random random
  - Regions regions
  - double sdThreshold
  - boolean verbose
- Constructor Detail
  - MeanCoverageEstimator(SAM sam, Regions regions)
- Method Detail
  - @groovy.transform.CompileStatic double estimate()
  - @groovy.transform.CompileStatic java.util.List<Region> generateRandomSamplingRegions()
  - static void main(java.lang.String[] args)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation