CoverageGaps

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.CoverageGaps

```
@groovy.util.logging.Log
class CoverageGaps
extends java.lang.Object
```
Discovers blocks of low coverage in a file output in BEDTools Coverage format, or alternatively MultiCov output.
Each low coverage block is output as a CoverageBlock object which has statistics about the coverage within the block. As CoverageBlock extends gngs.Region, you can easily turn this into a set of Regions to perform more calculations or statistics.
To use this class, create the object first by passing a file to compute coverage for, then call the calculate method to actually calculate the coverage blocks:
```
 CoverageGaps gaps = new CoverageGaps("test.cov.gz")
 gaps.calculate()
 println("There are " + gaps.blocks.size() + " low coverage regions")
 
```
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`int`	`BUFFER_SIZE_BYTES` Use a large buffer for very efficient reading
`CoverageBlock`	`block`
`int`	`blockCount`
`java.util.List<CoverageBlock>`	`blocks` Discovered gaps (the results) are stored here for access after calling calculate
`java.lang.String`	`coverageFilePath`
`CoverageStats`	`coveragePercentiles`
`org.apache.commons.math3.stat.descriptive.SummaryStatistics`	`coverageStats`
`RegulatingActor<CoverageBlock>`	`gapProcessor`
`int`	`lineCount`
`int`	`minRegionWidth` Only include gaps that are at least this size
`int`	`offset`
`java.lang.String`	`region`
`Regions`	`regions`
`int`	`threshold`
`int`	`totalBP`

Constructor Summary

Constructors
Constructor and description
`CoverageGaps ()`
`CoverageGaps (java.lang.String coverageFilePath)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.Object`	`asType(java.lang.Class clazz)`
	`void`	`calculate()`
	`void`	`calculateFromBEDTools(java.io.Reader reader)`
	`void`	`calculateFromMultiCov(java.io.Reader reader)`
	`void`	`calculateMultiCov()`
	`void`	`outputBlock(int endPos)`
	`void`	`processLine(java.lang.String chr, int start, int pos, int cov, java.lang.String id)`

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
  - int BUFFER_SIZE_BYTES
    
    Use a large buffer for very efficient reading
  - CoverageBlock block
  - int blockCount
  - java.util.List<CoverageBlock> blocks
    
    Discovered gaps (the results) are stored here for access after calling calculate
  - java.lang.String coverageFilePath
  - CoverageStats coveragePercentiles
  - org.apache.commons.math3.stat.descriptive.SummaryStatistics coverageStats
  - RegulatingActor<CoverageBlock> gapProcessor
  - int lineCount
  - int minRegionWidth
    
    Only include gaps that are at least this size
  - int offset
  - java.lang.String region
  - Regions regions
  - int threshold
  - int totalBP
- Constructor Detail
  - CoverageGaps()
  - CoverageGaps(java.lang.String coverageFilePath)
- Method Detail
  - @groovy.transform.CompileStatic java.lang.Object asType(java.lang.Class clazz)
  - void calculate()
  - @groovy.transform.CompileStatic void calculateFromBEDTools(java.io.Reader reader)
  - @groovy.transform.CompileStatic void calculateFromMultiCov(java.io.Reader reader)
  - void calculateMultiCov()
  - @groovy.transform.CompileStatic void outputBlock(int endPos)
  - @groovy.transform.CompileStatic void processLine(java.lang.String chr, int start, int pos, int cov, java.lang.String id)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation