Class CRAMDecoder

Method Details

• getFileFormat

  public final String 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 (see BundleResourceType and BundleResource.getFileFormat()).

  Specified by:

  getFileFormat in interface HtsDecoder<SAMFileHeader,SAMRecord>

  Returns:

  the name of the underlying file format handled by this decoder

• getDisplayName

  public final String getDisplayName()

  Description copied from interface: HtsDecoder

  Get a user-friendly display name for this decoder.

  Specified by:

  getDisplayName in interface HtsDecoder<SAMFileHeader,SAMRecord>

  Returns:

  a user-friendly display name for this decoder for use in error and warning messages

• getHeader

  public SAMFileHeader getHeader()

  Description copied from interface: HtsDecoder

  Get the file header for this decoder.

  Specified by:

  getHeader in interface HtsDecoder<SAMFileHeader,SAMRecord>

  Returns:

  the file header for this decoder, of type H

• close

  public void close()

  Description copied from interface: HtsDecoder

  Close any resources associated with this decoder.

  Specified by:

  close in interface AutoCloseable

  Specified by:

  close in interface Closeable

  Specified by:

  close in interface HtsDecoder<SAMFileHeader,SAMRecord>

• iterator

  public CloseableIterator<SAMRecord> iterator()

  Description copied from interface: HtsQuery

  Get an iterator of all records in the underlying resource.

  Specified by:

  iterator in interface HtsQuery<SAMRecord>

  Specified by:

  iterator in interface Iterable<SAMRecord>

  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.

  Specified by:

  isQueryable in interface HtsQuery<SAMRecord>

  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.

  Specified by:

  hasIndex in interface HtsQuery<SAMRecord>

  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.

  Specified by:

  query in interface HtsQuery<SAMRecord>

  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

  Specified by:

  queryStart in interface HtsQuery<SAMRecord>

  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.

  Specified by:

  queryUnmapped in interface ReadsDecoder

  Specified by:

  queryUnmapped in interface ReadsQuery<SAMRecord>

• 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.

  Specified by:

  queryMate in interface ReadsDecoder

  Specified by:

  queryMate in interface ReadsQuery<SAMRecord>

  Parameters:

  rec - the source record

  Returns:

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

• getInputBundle

  public Bundle getInputBundle()

  Get the input Bundle for this decoder.

  Returns:

  the input Bundle for this decoder

• getReadsDecoderOptions

  public ReadsDecoderOptions getReadsDecoderOptions()

  Get the ReadsDecoderOptions for this decoder.

  Returns:

  the ReadsDecoderOptions for this decoder.

• getCRAMReferenceSource

  @InternalAPI public static CRAMReferenceSource getCRAMReferenceSource(CRAMDecoderOptions cramDecoderOptions)