package api

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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 Iterable[SamRecord] 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.

Value Members

  1. object QueryType extends Enumeration

    Describes the two types of queries that can be performed.

  2. object SamOrder
  3. object SamRecord
  4. object SamSource

    Companion to the SamSource class that provides factory methods for sources.

  5. object SamWriter extends LazyLogging