SamBuilder

final def !=(arg0: Any): Boolean

final def ##(): Int

def +(other: String): String

def ++[B >: SamRecord, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def ++:[B >: SamRecord, That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def ++:[B >: SamRecord, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def ++=(that: Iterable[SamRecord]): Unit

Adds all the records from another builder to this one.

def ->[B](y: B): (SamBuilder, B)

def /:[B](z: B)(op: (B, SamRecord) ⇒ B): B

def :\[B](z: B)(op: (SamRecord, B) ⇒ B): B

final def ==(arg0: Any): Boolean

def addFrag(name: String = nextName, bases: String = randomBases, quals: String = defaultQuals, contig: Int = 0, start: Int = SAMRecord.NO_ALIGNMENT_START, unmapped: Boolean = false, cigar: String = readLength + "M", mapq: Int = 60, strand: Strand = Plus, attrs: Map[String, Any] = Map.empty): Option[SamRecord]

Adds a non-paired read.

def addPair(name: String = nextName, bases1: String = randomBases, bases2: String = randomBases, quals1: String = defaultQuals, quals2: String = defaultQuals, contig: Int = 0, start1: Int = SAMRecord.NO_ALIGNMENT_START, start2: Int = SAMRecord.NO_ALIGNMENT_START, unmapped1: Boolean = false, unmapped2: Boolean = false, cigar1: String = readLength + "M", cigar2: String = readLength + "M", mapq1: Int = 60, mapq2: Int = 60, strand1: Strand = Plus, strand2: Strand = Minus, attrs: Map[String, Any] = Map.empty): Seq[SamRecord]

Adds a pair of reads to the file.

def addString(b: StringBuilder): StringBuilder

def addString(b: StringBuilder, sep: String): StringBuilder

def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

def aggregate[B](z: ⇒ B)(seqop: (B, SamRecord) ⇒ B, combop: (B, B) ⇒ B): B

final def asInstanceOf[T0]: T0

val baseQuality: Int

def canEqual(that: Any): Boolean

def clone(): AnyRef

def collect[B, That](pf: PartialFunction[SamRecord, B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def collectFirst[B](pf: PartialFunction[SamRecord, B]): Option[B]

def companion: GenericCompanion[Iterable]

def copyToArray[B >: SamRecord](xs: Array[B], start: Int, len: Int): Unit

def copyToArray[B >: SamRecord](xs: Array[B]): Unit

def copyToArray[B >: SamRecord](xs: Array[B], start: Int): Unit

def copyToBuffer[B >: SamRecord](dest: Buffer[B]): Unit

def count(p: (SamRecord) ⇒ Boolean): Int

val defaultQuals: String

The default string of qualities to use.

def dict: SAMSequenceDictionary

Shorter accessor for the sequence dictionary.

def drop(n: Int): Iterable[SamRecord]

def dropRight(n: Int): Iterable[SamRecord]

def dropWhile(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]

def ensuring(cond: (SamBuilder) ⇒ Boolean, msg: ⇒ Any): SamBuilder

def ensuring(cond: (SamBuilder) ⇒ Boolean): SamBuilder

def ensuring(cond: Boolean, msg: ⇒ Any): SamBuilder

def ensuring(cond: Boolean): SamBuilder

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def exists(p: (SamRecord) ⇒ Boolean): Boolean

def filter(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]

def filterNot(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]

def finalize(): Unit

def find(p: (SamRecord) ⇒ Boolean): Option[SamRecord]

def flatMap[B, That](f: (SamRecord) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def flatten[B](implicit asTraversable: (SamRecord) ⇒ GenTraversableOnce[B]): Iterable[B]

def fold[A1 >: SamRecord](z: A1)(op: (A1, A1) ⇒ A1): A1

def foldLeft[B](z: B)(op: (B, SamRecord) ⇒ B): B

def foldRight[B](z: B)(op: (SamRecord, B) ⇒ B): B

def forall(p: (SamRecord) ⇒ Boolean): Boolean

def foreach[U](f: (SamRecord) ⇒ U): Unit

def formatted(fmtstr: String): String

def genericBuilder[B]: Builder[B, Iterable[B]]

final def getClass(): Class[_]

def groupBy[K](f: (SamRecord) ⇒ K): Map[K, Iterable[SamRecord]]

def grouped(size: Int): Iterator[Iterable[SamRecord]]

def hasDefiniteSize: Boolean

def hashCode(): Int

def head: SamRecord

def headOption: Option[SamRecord]

val header: SAMFileHeader

def init: Iterable[SamRecord]

def inits: Iterator[Iterable[SamRecord]]

def isEmpty: Boolean

final def isInstanceOf[T0]: Boolean

final def isTraversableAgain: Boolean

def iterator: Iterator[SamRecord]

Returns an iterator over the records that have been built.

def last: SamRecord

def lastOption: Option[SamRecord]

def map[B, That](f: (SamRecord) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def max[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord

def maxBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord

def min[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord

def minBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord

def mkString: String

def mkString(sep: String): String

def mkString(start: String, sep: String, end: String): String

final def ne(arg0: AnyRef): Boolean

def newBuilder: Builder[SamRecord, Iterable[SamRecord]]

def nextName: String

Generate a sequential name.

def nonEmpty: Boolean

final def notify(): Unit

final def notifyAll(): Unit

def par: ParIterable[SamRecord]

def parCombiner: Combiner[SamRecord, ParIterable[SamRecord]]

def partition(p: (SamRecord) ⇒ Boolean): (Iterable[SamRecord], Iterable[SamRecord])

def product[B >: SamRecord](implicit num: Numeric[B]): B

def randomBases: String

Generate a random sequence of bases of length readLength.

val readGroupId: Option[String]

val readLength: Int

def reduce[A1 >: SamRecord](op: (A1, A1) ⇒ A1): A1

def reduceLeft[B >: SamRecord](op: (B, SamRecord) ⇒ B): B

def reduceLeftOption[B >: SamRecord](op: (B, SamRecord) ⇒ B): Option[B]

def reduceOption[A1 >: SamRecord](op: (A1, A1) ⇒ A1): Option[A1]

def reduceRight[B >: SamRecord](op: (SamRecord, B) ⇒ B): B

def reduceRightOption[B >: SamRecord](op: (SamRecord, B) ⇒ B): Option[B]

def repr: Iterable[SamRecord]

def reversed: List[SamRecord]

val rg: SAMReadGroupRecord

def sameElements[B >: SamRecord](that: GenIterable[B]): Boolean

def scan[B >: SamRecord, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def scanLeft[B, That](z: B)(op: (B, SamRecord) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def scanRight[B, That](z: B)(op: (SamRecord, B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That

def seq: Iterable[SamRecord]

def size: Int

Returns the number of records that have been built.

def slice(from: Int, until: Int): Iterable[SamRecord]

def sliding(size: Int, step: Int): Iterator[Iterable[SamRecord]]

def sliding(size: Int): Iterator[Iterable[SamRecord]]

val sort: Option[SamOrder]

def span(p: (SamRecord) ⇒ Boolean): (Iterable[SamRecord], Iterable[SamRecord])

def splitAt(n: Int): (Iterable[SamRecord], Iterable[SamRecord])

def stringPrefix: String

def sum[B >: SamRecord](implicit num: Numeric[B]): B

final def synchronized[T0](arg0: ⇒ T0): T0

def tail: Iterable[SamRecord]

def tails: Iterator[Iterable[SamRecord]]

def take(n: Int): Iterable[SamRecord]

def takeRight(n: Int): Iterable[SamRecord]

def takeWhile(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]

def thisCollection: Iterable[SamRecord]

def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SamRecord, Col[SamRecord]]): Col[SamRecord]

def toArray[B >: SamRecord](implicit arg0: ClassTag[B]): Array[B]

def toBuffer[B >: SamRecord]: Buffer[B]

def toCollection(repr: Iterable[SamRecord]): Iterable[SamRecord]

def toIndexedSeq: IndexedSeq[SamRecord]

def toIterable: Iterable[SamRecord]

def toIterator: Iterator[SamRecord]

def toList: List[SamRecord]

def toMap[T, U](implicit ev: <:<[SamRecord, (T, U)]): Map[T, U]

def toParArray: ParArray[T]

def toSeq: Seq[SamRecord]

def toSet[B >: SamRecord]: Set[B]

def toSource: SamSource

Creates a SamReader over the records stored in a temporary file.

def toStream: Stream[SamRecord]

def toString(): String

def toTempFile(deleteOnExit: Boolean = true): FgBioDef.PathToBam

Writes the contents to a temporary file that will be deleted when the JVM exits.

def toTraversable: Traversable[SamRecord]

def toVector: Vector[SamRecord]

def transpose[B](implicit asTraversable: (SamRecord) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]

def unzip[A1, A2](implicit asPair: (SamRecord) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])

def unzip3[A1, A2, A3](implicit asTriple: (SamRecord) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])

def view(from: Int, until: Int): IterableView[SamRecord, Iterable[SamRecord]]

def view: IterableView[SamRecord, Iterable[SamRecord]]

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def withFilter(p: (SamRecord) ⇒ Boolean): FilterMonadic[SamRecord, Iterable[SamRecord]]

def write(path: FgBioDef.PathToBam): Unit

Writes the contents of the record set to the provided file path.

def zip[A1 >: SamRecord, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, B), That]): That

def zipAll[B, A1 >: SamRecord, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, B), That]): That

def zipWithIndex[A1 >: SamRecord, That](implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, Int), That]): That

def →[B](y: B): (SamBuilder, B)

def filter(p: (SamRecord) ⇒ Boolean): TraversableOnce[SamRecord]

def flatMap[B](f: (SamRecord) ⇒ GenTraversableOnce[B]): TraversableOnce[B]

def map[B](f: (SamRecord) ⇒ B): TraversableOnce[B]

def withFilter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]