Package htsjdk.beta.plugin.reads
Interface ReadsDecoder
- All Superinterfaces:
AutoCloseable
,Closeable
,HtsDecoder<SAMFileHeader,
,SAMRecord> HtsQuery<SAMRecord>
,Iterable<SAMRecord>
,ReadsQuery<SAMRecord>
- All Known Implementing Classes:
BAMDecoder
,BAMDecoderV1_0
,CRAMDecoder
,CRAMDecoderV2_1
,CRAMDecoderV3_0
,HtsgetBAMDecoder
,HtsgetBAMDecoderV1_2
,SAMDecoder
,SAMDecoderV1_0
Base class for all
HtsContentType.ALIGNED_READS
decoders. Defines the type parameters instantiated for
reads decoders.-
Method Summary
Modifier and TypeMethodDescriptionFetch the mate for the given read.Get an iterator of unmapped reads.Methods inherited from interface htsjdk.beta.plugin.HtsDecoder
close, getDisplayName, getFileFormat, 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
-
Method Details
-
queryUnmapped
CloseableIterator<SAMRecord> queryUnmapped()Get an iterator of unmapped reads. Requires an index resource to be included in the inputBundle
.- Specified by:
queryUnmapped
in interfaceReadsQuery<SAMRecord>
-
queryMate
Fetch the mate for the given read. Requires an index resource to be included in the inputBundle
.- Specified by:
queryMate
in interfaceReadsQuery<SAMRecord>
- Parameters:
rec
- the source record- Returns:
- the source record's mate, or Optional.empty() if the source record has no mate
-