package api
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Type Members
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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.
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sealed
trait
SamOrder
extends Product
Trait for specifying BAM orderings.
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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.
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class
SamRecordCodec
extends Codec[SamRecord]
Sorter.Codec implementation that wraps HTSJDK's BAMRecordCodec to read/write records to bytes.
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class
SamSource
extends IterableView[SamRecord, SamSource] with HeaderHelper with Closeable
A source class for reading SAM/BAM/CRAM files and for querying them.
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final
class
SamWriter
extends Closeable with Writer[SamRecord] with HeaderHelper
Provides the ability to write SamRecords to an output Path.
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class
TransientAttrs
extends AnyRef
Class that is used to provide a nice API to transient attributes in the SamRecord.