htsjdk.samtools

Class BAMRecordCodec

java.lang.Object

htsjdk.samtools.BAMRecordCodec

All Implemented Interfaces:

SortingCollection.Codec<SAMRecord>, java.lang.Cloneable

public class BAMRecordCodec
extends java.lang.Object
implements SortingCollection.Codec<SAMRecord>

Class for translating between in-memory and disk representation of BAMRecord.

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and 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.
void	setInputStream(java.io.InputStream is) Sets the input stream that records will be read from.
void	setInputStream(java.io.InputStream is, java.lang.String filename) Sets the input stream that records will be read from.
void	setOutputStream(java.io.OutputStream os) Sets the output stream that records will be written to.
void	setOutputStream(java.io.OutputStream os, java.lang.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 java.lang.Object

setOutputStream

public void setOutputStream(java.io.OutputStream os)

Sets the output stream that records will be written to.

Specified by:

setOutputStream in interface SortingCollection.Codec<SAMRecord>

setOutputStream

public void setOutputStream(java.io.OutputStream os,
                   java.lang.String filename)

Sets the output stream that records will be written to.

setInputStream

public void setInputStream(java.io.InputStream is)

Sets the input stream that records will be read from.

Specified by:

setInputStream in interface SortingCollection.Codec<SAMRecord>

setInputStream

public void setInputStream(java.io.InputStream is,
                  java.lang.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.

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.