java.lang.Object
- htsjdk.samtools.BAMRecordCodec

All Implemented Interfaces:

SortingCollection.Codec<SAMRecord>, Cloneable
```
public class BAMRecordCodec
extends Object
implements SortingCollection.Codec<SAMRecord>
```
Class for translating between in-memory and disk representation of BAMRecord.

Constructor Summary

Constructors
Constructor Description

BAMRecordCodec(SAMFileHeader header)

BAMRecordCodec(SAMFileHeader header, SAMRecordFactory factory)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`BAMRecordCodec`	`clone()`	Must return a cloned copy of the codec that can be used independently of the original instance.
`SAMRecord`	`decode()`	Read the next record from the input stream and convert into a java object.
`void`	`encode(SAMRecord alignment)`	Write object to OutputStream.
`static Cigar`	`makeSentinelCigar(Cigar cigar)`	Create a "Sentinel" cigar that will be placed in BAM file when the actual cigar has more than 0xffff operator, which are not supported by the bam format.
`void`	`setInputStream(InputStream is)`	Sets the input stream that records will be read from.
`void`	`setInputStream(InputStream is, String filename)`	Sets the input stream that records will be read from.
`void`	`setOutputStream(OutputStream os)`	Sets the output stream that records will be written to.
`void`	`setOutputStream(OutputStream os, String filename)`	Sets the output stream that records will be written to.

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

- Constructor Detail
  - BAMRecordCodec
```
public BAMRecordCodec(SAMFileHeader header)
```
  - BAMRecordCodec
```
public BAMRecordCodec(SAMFileHeader header,
                      SAMRecordFactory factory)
```
- Method Detail
  - clone
```
public BAMRecordCodec clone()
```
    Description copied from interface: SortingCollection.Codec
    
    Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.
    
    Specified by:
    
    clone in interface SortingCollection.Codec<SAMRecord>
    
    Overrides:
    
    clone in class Object
  - setOutputStream
```
public void setOutputStream(OutputStream os)
```
    Sets the output stream that records will be written to.
    
    Specified by:
    
    setOutputStream in interface SortingCollection.Codec<SAMRecord>
  - setOutputStream
```
public void setOutputStream(OutputStream os,
                            String filename)
```
    Sets the output stream that records will be written to.
  - setInputStream
```
public void setInputStream(InputStream is)
```
    Sets the input stream that records will be read from.
    
    Specified by:
    
    setInputStream in interface SortingCollection.Codec<SAMRecord>
  - setInputStream
```
public void setInputStream(InputStream is,
                           String filename)
```
    Sets the input stream that records will be read from.
  - encode
```
public void encode(SAMRecord alignment)
```
    Write object to OutputStream. Reference and mate reference indices must be resolvable, which either means that these have been set into the SAMRecord directly, or the SAMRecord must have a header assigned into it so that reference names can be resolved into indices.
    
    Specified by:
    
    encode in interface SortingCollection.Codec<SAMRecord>
    
    Parameters:
    
    alignment - Record to be written.
  - makeSentinelCigar
```
public static Cigar makeSentinelCigar(Cigar cigar)
```
    Create a "Sentinel" cigar that will be placed in BAM file when the actual cigar has more than 0xffff operator, which are not supported by the bam format. The actual cigar will be encoded and placed in the CG attribute.
    
    Parameters:
    
    cigar - actual cigar to create sentinel cigar for
    
    Returns:
    
    sentinel cigar xSyN with readLength (x) and referenceLength (y) matching the input cigar.
  - decode
```
public SAMRecord decode()
```
    Read the next record from the input stream and convert into a java object.
    
    Specified by:
    
    decode in interface SortingCollection.Codec<SAMRecord>
    
    Returns:
    
    null if no more records. Should throw exception if EOF is encountered in the middle of a record.

Constructor	Description
`BAMRecordCodec(SAMFileHeader header)`
`BAMRecordCodec(SAMFileHeader header, SAMRecordFactory factory)`

Class BAMRecordCodec

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BAMRecordCodec

BAMRecordCodec

Method Detail

clone

setOutputStream

setOutputStream

setInputStream

setInputStream

encode

makeSentinelCigar

decode