Package htsjdk.samtools

Class BAMRecordCodec

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

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 Details

BAMRecordCodec

public BAMRecordCodec(SAMFileHeader header)

BAMRecordCodec

public BAMRecordCodec(SAMFileHeader header,
 SAMRecordFactory factory)

Method Details

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.