htsjdk.beta.codecs.reads.bam.bamV1_0

Class BAMDecoderV1_0

java.lang.Object

htsjdk.beta.codecs.reads.bam.BAMDecoder

htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0

All Implemented Interfaces:

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

public class BAMDecoderV1_0
extends BAMDecoder

BAM v1.0 decoder.

Constructor Summary

Constructors

Constructor and Description
BAMDecoderV1_0(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Create a V1.0 BAM decoder for the given input bundle.

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
SAMFileHeader	getHeader() Get the file header for this decoder.
HtsVersion	getVersion() Get the version of the file format supported by 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 samRecord) 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 htsjdk.beta.codecs.reads.bam.BAMDecoder

getDisplayName, getFileFormat, getInputBundle, getReadsDecoderOptions

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.interval.HtsQuery

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

BAMDecoderV1_0

public BAMDecoderV1_0(Bundle inputBundle,
                      ReadsDecoderOptions readsDecoderOptions)

Create a V1.0 BAM decoder for the given input bundle. The primary resource in the bundle must have content type BundleResourceType.ALIGNED_READS, and the resource must be an appropriate format and version for this encoder (to find an encoder for a bundle, see ReadsResolver.

Parameters:

inputBundle - bundle to decoder

readsDecoderOptions - options to use

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsDecoder

Get the version of the file format supported by this decoder.

getHeader

public SAMFileHeader getHeader()

Description copied from interface: HtsDecoder

Get the file header for this decoder.

Returns:

the file header for this decoder, of type H

iterator

public CloseableIterator<SAMRecord> iterator()

Description copied from interface: HtsQuery

Get an iterator of all records in the underlying resource.

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.

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.

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.

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

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.

queryMate

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

Description copied from interface: ReadsDecoder

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

Parameters:

samRecord - the source record

Returns:

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

close

public void close()

Description copied from interface: HtsDecoder

Close any resources associated with this decoder.