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.
Trait for specifying BAM orderings.
A trait that fgbio uses as a replacement for SAMRecord.
Sorter.Codec implementation that wraps HTSJDK's BAMRecordCodec to read/write records to bytes.
A source class for reading SAM/BAM/CRAM files and for querying them.
Provides the ability to write SamRecords to an output Path.
Class that is used to provide a nice API to transient attributes in the 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.