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1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  var DefaultCompressionLevel: Int
5.  var DefaultCreateIndex: Boolean
6.  var DefaultMaxRecordsInRam: Int
7.  var DefaultUseAsyncIo: Boolean
8.  def apply(path: FgBioDef.PathToBam, header: SAMFileHeader, sort: Option[SamOrder] = None, ref: Option[FgBioDef.PathToFasta] = None, async: Boolean = DefaultUseAsyncIo, buffer: Int = Defaults.NON_ZERO_BUFFER_SIZE, compression: Int = DefaultCompressionLevel, tmp: Option[FgBioDef.DirPath] = None, maxRecordsInRam: Int = 1e6.toInt, index: Boolean = true, md5: Boolean = false, sortProgress: Option[ProgressLogger] = ..., writeProgress: Option[ProgressLogger] = ...): SamWriter

   Constructs a SamWriter for writing out SamRecords.

   Constructs a SamWriter for writing out SamRecords.

   path

   the path at which the data should be written

   header

   the header for the SAM/BAM

   sort

   an optional SamOrder into which to sort the reads. If no order is provided the reads are assumed to be in the order described in the header. If an order is provided the reads are _always_ sorted using that SamOrder before being emitted.

   ref

   an optional reference sequence for use in writing CRAM

   async

   if true use multiple threads to increase writing throughput

   buffer

   the buffer size, in bytes, to use for the writer

   compression

   the GZIP compression level to use when compressing data

   tmp

   an optional tmp directory to use when sorting

   maxRecordsInRam

   the maximum number of records to keep in RAM while sorting

   index

   if true, index the SAM/BAM file on the fly while writing

   md5

   if true, create an MD5 file for the output file while writing

   sortProgress

   an optional ProgressLogger to use if/when putting records into a Sorter

   writeProgress

   an optional ProgressLogger to use when writing records out

9.  final def asInstanceOf[T0]: T0

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10.  def clone(): AnyRef

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11.  final def eq(arg0: AnyRef): Boolean

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12.  def equals(arg0: Any): Boolean

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13.  def finalize(): Unit

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14.  final def getClass(): Class[_]

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15.  def hashCode(): Int

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16.  final def isInstanceOf[T0]: Boolean

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17.  lazy val logger: Logger

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18.  final def ne(arg0: AnyRef): Boolean

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19.  final def notify(): Unit

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20.  final def notifyAll(): Unit

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21.  final def synchronized[T0](arg0: ⇒ T0): T0

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22.  def toString(): String

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23.  final def wait(): Unit

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24.  final def wait(arg0: Long, arg1: Int): Unit

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25.  final def wait(arg0: Long): Unit

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