CramRecordReader (htsjdk 2.18.2 API)

java.lang.Object
- htsjdk.samtools.cram.encoding.reader.CramRecordReader

Direct Known Subclasses:

MultiRefSliceAlignmentSpanReader
```
public class CramRecordReader
extends Object
```

Field Summary

Fields
Modifier and Type Field Description

protected boolean APDelta

protected ValidationStringency validationStringency

Constructor Summary

Constructors
Constructor	Description
`CramRecordReader(BitInputStream coreInputStream, Map<Integer,ByteArrayInputStream> externalInputMap, CompressionHeader header, int refId, ValidationStringency validationStringency)`	Initialize a Cram Record Reader

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`read(CramCompressionRecord cramRecord)`	Read a Cram Compression Record, using this class's Encodings

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

- Field Detail
  - validationStringency
```
protected final ValidationStringency validationStringency
```
  - APDelta
```
protected final boolean APDelta
```
- Constructor Detail
  - CramRecordReader
```
public CramRecordReader(BitInputStream coreInputStream,
                        Map<Integer,ByteArrayInputStream> externalInputMap,
                        CompressionHeader header,
                        int refId,
                        ValidationStringency validationStringency)
```
    Initialize a Cram Record Reader
    
    Parameters:
    
    coreInputStream - Core data block bit stream, to be read by non-external Encodings
    
    externalInputMap - External data block byte stream map, to be read by external Encodings
    
    header - the associated Cram Compression Header
    
    refId - the reference sequence ID to assign to these records
    
    validationStringency - how strict to be when reading this CRAM record
- Method Detail
  - read
```
public void read(CramCompressionRecord cramRecord)
```
    Read a Cram Compression Record, using this class's Encodings
    
    Parameters:
    
    cramRecord - the Cram Compression Record to read into