Package htsjdk.samtools.cram.build

Class CRAMReferenceRegion

java.lang.Object

htsjdk.samtools.cram.build.CRAMReferenceRegion

public class CRAMReferenceRegion
extends Object

Holds a region/fragment of a reference contig. Maintains a CRAMReferenceSource for retrieving additional regions. This is a mutable object that is used to traverse along a reference contig via serial calls to either fetchReferenceBases(int) or fetchReferenceBasesByRegion(int, int, int). It caches the bases from the previous request, along with metadata about the (0-based) start offset, and length of the cached bases.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	UNINITIALIZED_LENGTH
static final int	UNINITIALIZED_START

Constructor Summary

Constructors

Constructor	Description
CRAMReferenceRegion(CRAMReferenceSource cramReferenceSource, SAMSequenceDictionary sequenceDictionary)

Method Summary

Modifier and Type	Method	Description
void	fetchReferenceBases(int referenceIndex)	Return the reference bases for an entire contig given a reference contig index.
void	fetchReferenceBasesByRegion(int referenceIndex, int zeroBasedStart, int requestedFragmentLength)	Get the reference bases for a region of a reference contig.
void	fetchReferenceBasesByRegion(AlignmentContext alignmentContext)	Fetch the bases to span an AlignmentContext.
byte[]	getCurrentReferenceBases()
int	getFullContigLength()
int	getReferenceIndex()
int	getRegionLength()
int	getRegionStart()
void	setEmbeddedReferenceBases(byte[] embeddedReferenceBases, int embeddedReferenceIndex, int zeroBasedStart)	Set this CRAMReferenceRegion to use an embedded reference.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

UNINITIALIZED_START

public static final int UNINITIALIZED_START

See Also:

• Constant Field Values

UNINITIALIZED_LENGTH

public static final int UNINITIALIZED_LENGTH

See Also:

• Constant Field Values

Constructor Details

CRAMReferenceRegion

public CRAMReferenceRegion(CRAMReferenceSource cramReferenceSource,
 SAMSequenceDictionary sequenceDictionary)

Parameters:

cramReferenceSource - CRAMReferenceSource to use to obtain reference bases

sequenceDictionary - SAMSequenceDictionary to use to resolve reference contig names to reference index

Method Details

getCurrentReferenceBases

public byte[] getCurrentReferenceBases()

Returns:

the currently cached reference bases (may return null)

getReferenceIndex

public int getReferenceIndex()

Returns:

the current reference index or ReferenceContext.UNINITIALIZED_REFERENCE_ID if no index has been established

getRegionStart

public int getRegionStart()

Returns:

the 0-based start position of the range of the current reference sequence region. UNINITIALIZED_START if no region has been established

getRegionLength

public int getRegionLength()

Returns:

the length of the current reference sequence region. UNINITIALIZED_LENGTH if no region has been established

fetchReferenceBases

public void fetchReferenceBases(int referenceIndex)

Return the reference bases for an entire contig given a reference contig index. Note: Serial calls to this method on behalf of non-coordinate sorted inputs can result in thrashing and poor performance due to repeated calls to the underlying CRAMReferenceSource, especially when the CRAMReferenceSource is fetching bases from a remote reference.

Parameters:

referenceIndex - the reference index for which bases should be retrieved.

Throws:

IllegalArgumentException - if the requested index is not present in the sequence dictionary or if the sequence's bases cannot be retrieved from the CRAMReferenceSource

fetchReferenceBasesByRegion

public void fetchReferenceBasesByRegion(int referenceIndex,
 int zeroBasedStart,
 int requestedFragmentLength)

Get the reference bases for a region of a reference contig. If the current region does not match the requested region, the referenceSource will be called to retrieve the bases. The caller cannot assume that the entire region requested is always fetched (if the requested range matches the alignment span for CRAM record or slice contains a CRAM records that is mapped beyond the end of the reference contig, fewer bases than were requested may be fetched.

Parameters:

referenceIndex - reference index for which to retrieve bases

zeroBasedStart - zero based start of the first base to be retrieved

requestedFragmentLength - length of the fragment to be retrieved

Throws:

IllegalArgumentException - if the requested sequence cannot be located in the sequence dictionary, or if the requested sequence cannot be provided by the underlying referenceSource

fetchReferenceBasesByRegion

public void fetchReferenceBasesByRegion(AlignmentContext alignmentContext)

Fetch the bases to span an AlignmentContext.

Parameters:

alignmentContext - the alignment context for which to fetch bases. must be an AlignmentContext for a single reference ReferenceContextType.SINGLE_REFERENCE_TYPE slice (see ReferenceContext.isMappedSingleRef())

setEmbeddedReferenceBases

public void setEmbeddedReferenceBases(byte[] embeddedReferenceBases,
 int embeddedReferenceIndex,
 int zeroBasedStart)

Set this CRAMReferenceRegion to use an embedded reference.

Parameters:

embeddedReferenceBases - the embedded reference bases to be used

embeddedReferenceIndex - the reference ID used in the slice containing the embedded reference

zeroBasedStart - the zero based reference start of the first base in the embedded reference bases

getFullContigLength

public int getFullContigLength()

Returns:

the length of the entire reference contig maintained by this region. note that this is not the same as the length of the current bases maintained by this region (this can happen if the region contains a fragment, or an embedded reference fragment), or -1 if no current region is established