case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[Alignment] with Product with Serializable
An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.
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def
read(is: InputStream): Iterator[Alignment]
Reads alignments from an input stream.
Reads alignments from an input stream. Autodetects SAM/BAM format.
- is
An InputStream connected to a process we are piping from.
- returns
Returns an iterator of Alignments read from the stream.
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- AnySAMOutFormatter → OutFormatter
- val stringency: ValidationStringency
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