Package 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>, Closeable, AutoCloseable, Iterable<SAMRecord>
public class SAMDecoderV1_0 extends SAMDecoder
SAM v1.0 decoder.

  • Constructor Details

    • 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.CT_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 Details

    • 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 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