htsjdk.beta.codecs.reads.cram

Class CRAMDecoder

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMDecoder

All Implemented Interfaces:

HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, ReadsDecoder, ReadsQuery<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<SAMRecord>

Direct Known Subclasses:

CRAMDecoderV2_1, CRAMDecoderV3_0

@InternalAPI
public abstract class CRAMDecoder
extends java.lang.Object
implements ReadsDecoder

InternalAPI Base class for BundleResourceType.READS_CRAM decoders.

Constructor Summary

Constructors

Constructor and Description
CRAMDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) InternalAPI Common constructor for CRAM decoders.

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
static CRAMReferenceSource	getCRAMReferenceSource(CRAMDecoderOptions cramDecoderOptions)
java.lang.String	getDisplayName() Get a user-friendly display name for this decoder.
java.lang.String	getFileFormat() Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).
SAMFileHeader	getHeader() Get the file header for this decoder.
Bundle	getInputBundle() Get the input Bundle for this decoder.
ReadsDecoderOptions	getReadsDecoderOptions() Get the ReadsDecoderOptions for this decoder.
boolean	hasIndex() Return true if the underlying resource has an index.
boolean	isQueryable() Gte true if the underlying resource is queryable.
CloseableIterator<SAMRecord>	iterator() Get an iterator of all records in the underlying resource.
CloseableIterator<SAMRecord>	query(java.util.List<HtsInterval> intervals, HtsQueryRule queryRule) Get an iterator over all records from the underlying resource that match the query arguments.
java.util.Optional<SAMRecord>	queryMate(SAMRecord rec) Fetch the mate for the given read.
CloseableIterator<SAMRecord>	queryStart(java.lang.String queryName, long start) Get an iterator over all records from the underlying resource that overlap the start position
CloseableIterator<SAMRecord>	queryUnmapped() Get an iterator of unmapped reads.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.HtsDecoder

getVersion

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery

query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

CRAMDecoder

@InternalAPI
public CRAMDecoder(Bundle inputBundle,
                                ReadsDecoderOptions readsDecoderOptions)

InternalAPI Common constructor for CRAM decoders.

Parameters:

inputBundle - an Bundle containing cram resource

readsDecoderOptions - ReadsDecoderOptions to use.

Method Detail

getFileFormat

public final java.lang.String getFileFormat()

Description copied from interface: HtsDecoder

Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).

Specified by:

getFileFormat in interface HtsDecoder<SAMFileHeader,SAMRecord>

Returns:

the name of the underlying file format handled by this decoder

getDisplayName

public final java.lang.String getDisplayName()

Description copied from interface: HtsDecoder

Get a user-friendly display name for this decoder.

Specified by:

getDisplayName in interface HtsDecoder<SAMFileHeader,SAMRecord>

Returns:

a user-friendly display name for this decoder for use in error and warning messages

getHeader

public SAMFileHeader getHeader()

Description copied from interface: HtsDecoder

Get the file header for this decoder.

Specified by:

getHeader in interface HtsDecoder<SAMFileHeader,SAMRecord>

Returns:

the file header for this decoder, of type H

close

public void close()

Description copied from interface: HtsDecoder

Close any resources associated with this decoder.

Specified by:

close in interface HtsDecoder<SAMFileHeader,SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

iterator

public CloseableIterator<SAMRecord> iterator()

Description copied from interface: HtsQuery

Get an iterator of all records in the underlying resource.

Specified by:

iterator in interface HtsQuery<SAMRecord>

Specified by:

iterator in interface java.lang.Iterable<SAMRecord>

Returns:

an iterator of all records in the underlying resource

isQueryable

public boolean isQueryable()

Description copied from interface: HtsQuery

Gte true if the underlying resource is queryable.

Specified by:

isQueryable in interface HtsQuery<SAMRecord>

Returns:

true if the underlying resource is queryable. this may be true even if the underlying resource returns false for HtsQuery.hasIndex()

hasIndex

public boolean hasIndex()

Description copied from interface: HtsQuery

Return true if the underlying resource has an index.

Specified by:

hasIndex in interface HtsQuery<SAMRecord>

Returns:

true if the underlying resource has an index

query

public CloseableIterator<SAMRecord> query(java.util.List<HtsInterval> intervals,
                                          HtsQueryRule queryRule)

Description copied from interface: HtsQuery

Get an iterator over all records from the underlying resource that match the query arguments. Callers much ensure that the intervals are in increasing order and do not overlap or abut.

Specified by:

query in interface HtsQuery<SAMRecord>

Parameters:

intervals - list of intervals to match

queryRule - query rule to use, from HtsQueryRule

Returns:

an iterator over all records from the underlying resource that match the query arguments

queryStart

public CloseableIterator<SAMRecord> queryStart(java.lang.String queryName,
                                               long start)

Description copied from interface: HtsQuery

Get an iterator over all records from the underlying resource that overlap the start position

Specified by:

queryStart in interface HtsQuery<SAMRecord>

Parameters:

queryName - name to match

start - start position to overlap

Returns:

an iterator over all records from the underlying resource that overlap the start position

queryUnmapped

public CloseableIterator<SAMRecord> queryUnmapped()

Description copied from interface: ReadsDecoder

Get an iterator of unmapped reads. Requires an index resource to be included in the input Bundle.

Specified by:

queryUnmapped in interface ReadsDecoder

Specified by:

queryUnmapped in interface ReadsQuery<SAMRecord>

queryMate

public java.util.Optional<SAMRecord> queryMate(SAMRecord rec)

Description copied from interface: ReadsDecoder

Fetch the mate for the given read. Requires an index resource to be included in the input Bundle.

Specified by:

queryMate in interface ReadsDecoder

Specified by:

queryMate in interface ReadsQuery<SAMRecord>

Parameters:

rec - the source record

Returns:

the source record's mate, or Optional.empty() if the source record has no mate

getInputBundle

public Bundle getInputBundle()

Get the input Bundle for this decoder.

Returns:

the input Bundle for this decoder

getReadsDecoderOptions

public ReadsDecoderOptions getReadsDecoderOptions()

Get the ReadsDecoderOptions for this decoder.

Returns:

the ReadsDecoderOptions for this decoder.

getCRAMReferenceSource

@InternalAPI
public static CRAMReferenceSource getCRAMReferenceSource(CRAMDecoderOptions cramDecoderOptions)