Type Members

1.  final class SamIterator extends SelfClosingIterator[SamRecord] with HeaderHelper

   An iterator over SamRecords that will automatically close the underlying iterator at the end of iteration, and provides access to the SAMFileHeader from the associated source.

2.  sealed trait SamOrder extends Product

   Trait for specifying BAM orderings.

3.  trait SamRecord extends AnyRef

   A trait that fgbio uses as a replacement for SAMRecord.

   A trait that fgbio uses as a replacement for SAMRecord. The trait is self-typed as a SamRecordIntermediate which is a sub-class of SAMRecord. It is done this wasy so that a) we can access superclass methods via SamRecordIntermediate but that self-typing here instead of extending hides the SAMRecord API from users of the class. The result is always a SAMRecord but isn't seen as such without casting.

4.  class SamRecordCodec extends Codec[SamRecord]

   Sorter.Codec implementation that wraps HTSJDK's BAMRecordCodec to read/write records to bytes.

5.  class SamSource extends IterableView[SamRecord, SamSource] with HeaderHelper with Closeable

   A source class for reading SAM/BAM/CRAM files and for querying them.

6.  final class SamWriter extends Closeable with Writer[SamRecord] with HeaderHelper

   Provides the ability to write SamRecords to an output Path.

7.  class TransientAttrs extends AnyRef

   Class that is used to provide a nice API to transient attributes in the SamRecord.