Package htsjdk.beta.codecs.reads.sam
Class SAMDecoder
java.lang.Object
htsjdk.beta.codecs.reads.sam.SAMDecoder
- All Implemented Interfaces:
HtsDecoder<SAMFileHeader,
,SAMRecord> HtsQuery<SAMRecord>
,ReadsDecoder
,ReadsQuery<SAMRecord>
,Closeable
,AutoCloseable
,Iterable<SAMRecord>
- Direct Known Subclasses:
SAMDecoderV1_0
InternalAPI
Base class for
BundleResourceType.READS_SAM
decoders.-
Constructor Summary
ConstructorDescriptionSAMDecoder
(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Create a SAM decoder for the given input bundle. -
Method Summary
Modifier and TypeMethodDescriptionfinal String
Get a user-friendly display name for this decoder.final String
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 (seeBundleResourceType
andBundleResource.getFileFormat()
).Get the inputBundle
for this decoder.Get theReadsDecoderOptions
for this decoder.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
close, getHeader, getVersion
Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
hasIndex, isQueryable, iterator, query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface htsjdk.beta.plugin.reads.ReadsDecoder
queryMate, queryUnmapped
-
Constructor Details
-
SAMDecoder
Create a SAM decoder for the given input bundle. The primary resource in the bundle must have content typeBundleResourceType.ALIGNED_READS
, and the resource must be an appropriate format and version for this encoder (to find an encoder for a bundle, seeReadsResolver
.- Parameters:
inputBundle
- inputBundle
to decodereadsDecoderOptions
-ReadsDecoderOptions
to use
-
-
Method Details
-
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 (seeBundleResourceType
andBundleResource.getFileFormat()
).- Specified by:
getFileFormat
in interfaceHtsDecoder<SAMFileHeader,
SAMRecord> - Returns:
- the name of the underlying file format handled by this decoder
-
getDisplayName
Description copied from interface:HtsDecoder
Get a user-friendly display name for this decoder.- Specified by:
getDisplayName
in interfaceHtsDecoder<SAMFileHeader,
SAMRecord> - Returns:
- a user-friendly display name for this decoder for use in error and warning messages
-
getInputBundle
Get the inputBundle
for this decoder.- Returns:
- the input
Bundle
for this decoder
-
getReadsDecoderOptions
Get theReadsDecoderOptions
for this decoder.- Returns:
- the
ReadsDecoderOptions
for this decoder.
-