MultiCov

Summary:
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Constructor
Method

| Detail:
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Constructor
Method

gngs.tools.MultiCov

```
@groovy.util.logging.Log
class MultiCov
extends ToolBase
```
A command line tool to rapidly calculate per-base coverage across multiple BAM files with extended support for coverage normalisation and variability calculation.
MultiCov reads BAM files directly and calculates the coverage over a specified set of regions. It is designed to ensure reading, writing and coverage calculation are all highly parallelised for maximum performance.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`static java.lang.String`	`OVERVIEW`
`java.util.List<SAM>`	`bams`
`java.util.List`	`cvThresholds`
`java.text.NumberFormat`	`fmt`
`java.util.Map<java.lang.String, java.lang.Double>`	`means` Means calculated as part of the 2-pass mean estimation phase
`int`	`minimumMapQ`
`boolean`	`phase1`
`Regions`	`scanRegions`
`int`	`statsMaxPctValue`

Constructor Summary

Constructors
Constructor and description
`MultiCov ()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`Regions`	`filterToBAMContigs(Regions regions)`
	`java.util.List<java.util.Map>`	`interpolateGCProfile(java.util.List<java.util.Map> gc)`
	`static void`	`main(java.lang.String[] args)`
	`Regions`	`resolveRegionsToScan()` Combine the various possible options for specifying which region to analyse into a single regions object (see scanRegions).
	`void`	`run()`
	`void`	`run(gngs.coverage.CoverageSummarizer summarizer, boolean skipEstimateMeans)` Parameters: summarizer

- Property Detail
  - static java.lang.String OVERVIEW
  - java.util.List<SAM> bams
  - final java.util.List cvThresholds
  - java.text.NumberFormat fmt
  - java.util.Map<java.lang.String, java.lang.Double> means
    
    Means calculated as part of the 2-pass mean estimation phase
  - int minimumMapQ
  - boolean phase1
  - Regions scanRegions
  - int statsMaxPctValue
- Constructor Detail
  - MultiCov()
- Method Detail
  - @groovy.transform.CompileStatic Regions filterToBAMContigs(Regions regions)
  - java.util.List<java.util.Map> interpolateGCProfile(java.util.List<java.util.Map> gc)
  - static void main(java.lang.String[] args)
  - Regions resolveRegionsToScan()
    
    Combine the various possible options for specifying which region to analyse into a single regions object (see scanRegions).
  - @java.lang.Override void run()
  - void run(gngs.coverage.CoverageSummarizer summarizer, boolean skipEstimateMeans)
    
    Parameters:
    summarizer
    skipEstimateMeans - if set to false, determine whether to estimate means automatically

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation