object SamSource
Companion to the SamSource class that provides factory methods for sources.
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- var DefaultUseAsyncIo: Boolean
- var DefaultValidationStringency: ValidationStringency
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def
apply(path: FgBioDef.PathToBam, index: Option[FgBioDef.FilePath] = None, ref: Option[FgBioDef.PathToFasta] = None, async: Boolean = DefaultUseAsyncIo, stringency: ValidationStringency = DefaultValidationStringency, factory: SAMRecordFactory = SamRecord.Factory): SamSource
Constructs a SamSource to read from the provided path.
Constructs a SamSource to read from the provided path.
- path
the path to read the SAM/BAM/CRAM from
- index
an optional path to read the index from
- ref
an optional reference sequencing for decoding CRAM files
- async
if true use extra thread(s) to speed up reading
- stringency
the validation stringency to apply when reading the data
- factory
a SAMRecordFactory; MUST return classes that mix in SamRecord
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