htsjdk.beta.codecs.reads.sam.samV1_0

Class SAMDecoderV1_0

java.lang.Object

htsjdk.beta.codecs.reads.sam.SAMDecoder

htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0

All Implemented Interfaces:

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

public class SAMDecoderV1_0
extends SAMDecoder

SAM v1.0 decoder.

Constructor Summary

Constructors

Constructor and Description
SAMDecoderV1_0(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Create a V1.0 SAM 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.
java.util.Optional<SAMRecord>	queryMate(SAMRecord rec) Fetch the mate for the given read.
CloseableIterator<SAMRecord>	queryUnmapped() Get an iterator of unmapped reads.

Methods inherited from class htsjdk.beta.codecs.reads.sam.SAMDecoder

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

SAMDecoderV1_0

public SAMDecoderV1_0(Bundle inputBundle,
                      ReadsDecoderOptions readsDecoderOptions)

Create a V1.0 SAM 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

close

public void close()

Description copied from interface: HtsDecoder

Close any resources associated with this decoder.

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 rec)

Description copied from interface: ReadsDecoder

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

Parameters:

rec - the source record

Returns:

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