CountReadsOnMarkers (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.coverage.CountReadsOnMarkers

```
public class CountReadsOnMarkers
extends java.lang.Object
```
Count how many reads map (from many SAM/BAM files) onto markers

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

static boolean debug

static int MAX_EXONS_CHART

static int SHOW_EVERY

Constructor Summary

Constructors
Constructor Description

CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addFile(java.lang.String samFileName)`	Add a SAM/BAM file to be processed
`void`	`addMarkerType(Marker marker, java.lang.String type)`
`void`	`count()`	Count markers from all files
`MarkerTypes`	`getMarkerTypes()`
`int`	`getReadLengthAvg()`	Average read length
`java.lang.String`	`html()`	Show charts in html
`java.lang.String`	`probabilityTable(CountByType prob)`	Show probabilities
`void`	`setVerbose(boolean verbose)`
`java.lang.String`	`toString()`	Print table to STDOUT

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SHOW_EVERY
```
public static final int SHOW_EVERY
```
See Also:

Constant Field Values

MAX_EXONS_CHART
```
public static final int MAX_EXONS_CHART
```
See Also:

Constant Field Values

debug
```
public static boolean debug
```

Constructor Detail

CountReadsOnMarkers

public CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)

Method Detail

addFile
```
public void addFile(java.lang.String samFileName)
```
Add a SAM/BAM file to be processed

Parameters:

samFileName -

addMarkerType

public void addMarkerType(Marker marker,
                          java.lang.String type)

count
```
public void count()
```
Count markers from all files

getMarkerTypes
```
public MarkerTypes getMarkerTypes()
```

getReadLengthAvg
```
public int getReadLengthAvg()
```
Average read length

Returns:

html
```
public java.lang.String html()
```
Show charts in html

Returns:

probabilityTable
```
public java.lang.String probabilityTable(CountByType prob)
```
Show probabilities

Parameters:

prob - : Probabilities for each

Returns:

A string showing a tab delimited table

setVerbose

public void setVerbose(boolean verbose)

toString
```
public java.lang.String toString()
```
Print table to STDOUT

Overrides:

toString in class java.lang.Object