SVDReadCountPanelOfNormals (gatk 4.1.7.0 API)

All Known Implementing Classes:

HDF5SVDReadCountPanelOfNormals
```
public interface SVDReadCountPanelOfNormals
```
Interface for the panel of normals (PoN) for SVD-based coverage denoising.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`default SVDDenoisedCopyRatioResult`	`denoise(SimpleCountCollection readCounts, int numEigensamples)` Standardizes and denoises `readCounts` using `numEigensamples` of the eigensamples.
`double[][]`	`getEigensampleVectors()` Returns a modifiable copy of an array containing the orthnonormal matrix of eigensample vectors.
`int`	`getNumEigensamples()` Returns the number of eigensamples.
`double[]`	`getOriginalIntervalGCContent()` Returns a modifiable copy of an array containing the GC content of the original intervals (in the same order as in `getOriginalIntervals()`).
`java.util.List<SimpleInterval>`	`getOriginalIntervals()` Returns a modifiable copy of the list of the original intervals that were used to build this PoN (no filtering will have been applied).
`double[][]`	`getOriginalReadCounts()` Returns a modifiable copy of the original matrix of integer read-counts (represented as doubles) used to build the PoN (no filtering will have been applied).
`double[]`	`getPanelIntervalFractionalMedians()` Returns a modifiable copy of an array containing the median (across all samples, before filtering) of the fractional coverage at each panel interval (in the same order as in `getPanelIntervals()`).
`java.util.List<SimpleInterval>`	`getPanelIntervals()` Returns a modifiable copy of the list of the intervals contained in this PoN after all filtering has been applied.
`htsjdk.samtools.SAMSequenceDictionary`	`getSequenceDictionary()` Returns the sequence dictionary common to all of the read counts used to build the PoN.
`double[]`	`getSingularValues()` Returns a modifiable copy of an array of the singular values of the eigensamples in decreasing order.
`double`	`getVersion()` Returns the PoN version.

- Method Detail
  - getVersion
```
double getVersion()
```
    Returns the PoN version.
  - getNumEigensamples
```
int getNumEigensamples()
```
    Returns the number of eigensamples.
  - getSequenceDictionary
```
htsjdk.samtools.SAMSequenceDictionary getSequenceDictionary()
```
    Returns the sequence dictionary common to all of the read counts used to build the PoN.
  - getOriginalReadCounts
```
double[][] getOriginalReadCounts()
```
    Returns a modifiable copy of the original matrix of integer read-counts (represented as doubles) used to build the PoN (no filtering will have been applied). This matrix has has dimensions M_original x N_original, where M_original is the number of original intervals and N_original is the number of original samples.
  - getOriginalIntervals
```
java.util.List<SimpleInterval> getOriginalIntervals()
```
    Returns a modifiable copy of the list of the original intervals that were used to build this PoN (no filtering will have been applied). This list has length M_original.
  - getOriginalIntervalGCContent
```
double[] getOriginalIntervalGCContent()
```
    Returns a modifiable copy of an array containing the GC content of the original intervals (in the same order as in getOriginalIntervals()). This array has length M_original.
  - getPanelIntervals
```
java.util.List<SimpleInterval> getPanelIntervals()
```
    Returns a modifiable copy of the list of the intervals contained in this PoN after all filtering has been applied. This list has length M.
  - getPanelIntervalFractionalMedians
```
double[] getPanelIntervalFractionalMedians()
```
    Returns a modifiable copy of an array containing the median (across all samples, before filtering) of the fractional coverage at each panel interval (in the same order as in getPanelIntervals()). This is used to standardize samples. This array has length M.
  - getSingularValues
```
double[] getSingularValues()
```
    Returns a modifiable copy of an array of the singular values of the eigensamples in decreasing order. This array has length K.
    
    Throws:
    
    java.lang.UnsupportedOperationException - if the panel only contains a single sample or if no eigensamples were requested upon panel creation
  - getEigensampleVectors
```
double[][] getEigensampleVectors()
```
    Returns a modifiable copy of an array containing the orthnonormal matrix of eigensample vectors. This matrix has has dimensions M x K, where M is the number of panel intervals (after filtering) and K is the number of eigensamples. Columns are sorted by singular value in decreasing order.
    
    Throws:
    
    java.lang.UnsupportedOperationException - if the panel only contains a single sample or if no eigensamples were requested upon panel creation
  - denoise
```
default SVDDenoisedCopyRatioResult denoise(SimpleCountCollection readCounts,
                                           int numEigensamples)
```
    Standardizes and denoises readCounts using numEigensamples of the eigensamples. If no eigensamples are available, the denoised output should be identical to the standardized output.

Interface SVDReadCountPanelOfNormals

Method Summary

Method Detail

getVersion

getNumEigensamples

getSequenceDictionary

getOriginalReadCounts

getOriginalIntervals

getOriginalIntervalGCContent

getPanelIntervals

getPanelIntervalFractionalMedians

getSingularValues

getEigensampleVectors

denoise