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>, Closeable, AutoCloseable, Iterable<SAMRecord>

public class BAMDecoderV1_0 extends BAMDecoder
BAM v1.0 decoder.
  • Constructor Details

    • 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.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
    • query

      public CloseableIterator<SAMRecord> query(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(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 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.