Sam2CramRecordFactory (htsjdk 2.18.2 API)

java.lang.Object
- htsjdk.samtools.cram.build.Sam2CramRecordFactory

public class Sam2CramRecordFactory
extends Object

Field Summary

Fields
Modifier and Type Field Description

boolean captureAllTags

Set<String> captureTags

Set<String> ignoreTags

boolean preserveReadNames

Constructor Summary

Constructors
Constructor Description

Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader, Version version)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`CramCompressionRecord`	`createCramRecord(SAMRecord record)`	Create a CramCompressionRecord.
`long`	`getBaseCount()`
`long`	`getFeatureCount()`
`Map<String,Integer>`	`getReadGroupMap()`
`byte[]`	`getRefBases()`
`void`	`setRefBases(byte[] refBases)`

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

Field Detail

captureAllTags
```
public boolean captureAllTags
```

preserveReadNames
```
public boolean preserveReadNames
```

captureTags
```
public final Set<String> captureTags
```

ignoreTags
```
public final Set<String> ignoreTags
```

Constructor Detail

Sam2CramRecordFactory

public Sam2CramRecordFactory(byte[] refBases,
                             SAMFileHeader samFileHeader,
                             Version version)

Method Detail
- createCramRecord
```
public CramCompressionRecord createCramRecord(SAMRecord record)
```
  Create a CramCompressionRecord.
  
  Parameters:
  
  record - If the input record does not have an associated SAMFileHeader, it will be updated with the header used for the factory in order to allow reference indices to be resolved.
  
  Returns:
  
  CramCompressionRecord
- getRefBases
```
public byte[] getRefBases()
```
- setRefBases
```
public void setRefBases(byte[] refBases)
```
- getReadGroupMap
```
public Map<String,Integer> getReadGroupMap()
```
- getBaseCount
```
public long getBaseCount()
```
- getFeatureCount
```
public long getFeatureCount()
```