trait SamRecord extends AnyRef
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.
- Self Type
- SamRecord with SamRecordIntermediate
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- SamRecord
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Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
- def +(other: String): String
- def ->[B](y: B): (SamRecord, B)
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
apply[A](name: String): A
- Annotations
- @inline()
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
asSam: SAMRecord
Returns this record as a SAMRecord.
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final
def
attributes: Map[String, Any]
- Annotations
- @inline()
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final
def
bases: Array[Byte]
- Annotations
- @inline()
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final
def
basesString: String
- Annotations
- @inline()
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final
def
bases_=(bs: String): Unit
- Annotations
- @inline()
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final
def
bases_=(bs: Array[Byte]): Unit
- Annotations
- @inline()
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final
def
cigar: Cigar
- Annotations
- @inline()
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final
def
cigarChanged(cigar: String): Unit
- Annotations
- @inline()
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final
def
cigar_=(cig: Cigar): Unit
- Annotations
- @inline()
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final
def
cigar_=(cig: String): Unit
- Annotations
- @inline()
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def
clone(): SamRecord
Clone method that does a "reasonably deep" clone.
Clone method that does a "reasonably deep" clone. The bases and quals are cloned as is the attributes map, though not the values in the attributes map.
- Definition Classes
- SamRecord → AnyRef
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final
def
contains(name: String): Boolean
- Annotations
- @inline()
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final
def
duplicate: Boolean
- Annotations
- @inline()
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final
def
duplicate_=(dupe: Boolean): Unit
- Annotations
- @inline()
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final
def
end: Int
- Annotations
- @inline()
- def ensuring(cond: (SamRecord) ⇒ Boolean, msg: ⇒ Any): SamRecord
- def ensuring(cond: (SamRecord) ⇒ Boolean): SamRecord
- def ensuring(cond: Boolean, msg: ⇒ Any): SamRecord
- def ensuring(cond: Boolean): SamRecord
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
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final
def
firstOfPair: Boolean
- Annotations
- @inline()
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final
def
firstOfPair_=(first: Boolean): Unit
- Annotations
- @inline()
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final
def
flags: Int
- Annotations
- @inline()
- def formatted(fmtstr: String): String
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final
def
get[A](name: String): Option[A]
- Annotations
- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
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final
def
getOrElse[A](name: String, default: ⇒ A): A
- Annotations
- @inline()
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def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
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final
def
header: SAMFileHeader
- Annotations
- @inline()
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final
def
header_=(header: SAMFileHeader): Unit
- Annotations
- @inline()
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def
id: String
Returns a string that is useful to identify a SamRecord, mostly for testing and error messages.
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final
def
insertSize: Int
- Annotations
- @inline()
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final
def
insertSize_=(s: Int): Unit
- Annotations
- @inline()
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def
isFrPair: Boolean
Returns true if the read is mapped in an FR pair, false otherwise.
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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final
def
length: Int
- Annotations
- @inline()
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final
def
mapped: Boolean
- Annotations
- @inline()
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final
def
mapped_=(mapped: Boolean): Unit
- Annotations
- @inline()
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final
def
mapq: Int
- Annotations
- @inline()
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final
def
mapq_=(q: Int): Unit
- Annotations
- @inline()
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final
def
mateEnd: Option[Int]
- Annotations
- @inline()
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final
def
mateMapped: Boolean
- Annotations
- @inline()
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final
def
mateMapped_=(mapped: Boolean): Unit
- Annotations
- @inline()
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final
def
mateNegativeStrand: Boolean
- Annotations
- @inline()
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final
def
mateNegativeStrand_=(negative: Boolean): Unit
- Annotations
- @inline()
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final
def
matePositiveStrand: Boolean
- Annotations
- @inline()
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final
def
matePositiveStrand_=(positive: Boolean): Unit
- Annotations
- @inline()
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final
def
mateRefIndex: Int
- Annotations
- @inline()
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final
def
mateRefIndex_=(index: Int): Unit
- Annotations
- @inline()
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final
def
mateRefName: String
- Annotations
- @inline()
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final
def
mateRefName_=(name: String): Unit
- Annotations
- @inline()
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final
def
mateStart: Int
- Annotations
- @inline()
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final
def
mateStart_=(s: Int): Unit
- Annotations
- @inline()
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final
def
mateUnmapped: Boolean
- Annotations
- @inline()
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final
def
mateUnmapped_=(unmapped: Boolean): Unit
- Annotations
- @inline()
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final
def
name: String
- Annotations
- @inline()
-
final
def
name_=(name: String): Unit
- Annotations
- @inline()
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
negativeStrand: Boolean
- Annotations
- @inline()
-
final
def
negativeStrand_=(negative: Boolean): Unit
- Annotations
- @inline()
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
def
pairOrientation: PairOrientation
Gets the PairOrientation of the record.
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final
def
paired: Boolean
- Annotations
- @inline()
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final
def
paired_=(paired: Boolean): Unit
- Annotations
- @inline()
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final
def
pf: Boolean
- Annotations
- @inline()
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final
def
pf_=(pf: Boolean): Unit
- Annotations
- @inline()
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final
def
positiveStrand: Boolean
- Annotations
- @inline()
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final
def
positiveStrand_=(positive: Boolean): Unit
- Annotations
- @inline()
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final
def
properlyPaired: Boolean
- Annotations
- @inline()
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final
def
properlyPaired_=(paired: Boolean): Unit
- Annotations
- @inline()
-
final
def
quals: Array[Byte]
- Annotations
- @inline()
-
final
def
qualsString: String
- Annotations
- @inline()
-
final
def
quals_=(qs: String): Unit
- Annotations
- @inline()
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final
def
quals_=(qs: Array[Byte]): Unit
- Annotations
- @inline()
-
final
def
readGroup: SAMReadGroupRecord
- Annotations
- @inline()
-
final
def
readPosAtRefPos(pos: Int, returnLastBaseIfDeleted: Boolean): Int
- Annotations
- @inline()
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final
def
refIndex: Int
- Annotations
- @inline()
-
final
def
refIndex_=(index: Int): Unit
- Annotations
- @inline()
-
final
def
refName: String
- Annotations
- @inline()
-
final
def
refName_=(name: String): Unit
- Annotations
- @inline()
-
final
def
refPosAtReadPos(pos: Int): Int
- Annotations
- @inline()
-
final
def
remove(name: String): Unit
- Annotations
- @inline()
-
final
def
secondOfPair: Boolean
- Annotations
- @inline()
-
final
def
secondOfPair_=(second: Boolean): Unit
- Annotations
- @inline()
-
final
def
secondary: Boolean
- Annotations
- @inline()
-
final
def
secondary_=(secondary: Boolean): Unit
- Annotations
- @inline()
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final
def
start: Int
- Annotations
- @inline()
-
final
def
start_=(s: Int): Unit
- Annotations
- @inline()
-
final
def
supplementary: Boolean
- Annotations
- @inline()
-
final
def
supplementary_=(supplementary: Boolean): Unit
- Annotations
- @inline()
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
final
def
transientAttrs: TransientAttrs
- Annotations
- @inline()
-
final
def
unclippedEnd: Int
- Annotations
- @inline()
-
final
def
unclippedStart: Int
- Annotations
- @inline()
-
final
def
unmapped: Boolean
- Annotations
- @inline()
-
final
def
unmapped_=(unmapped: Boolean): Unit
- Annotations
- @inline()
-
final
def
unpaired: Boolean
- Annotations
- @inline()
-
final
def
unpaired_=(unpaired: Boolean): Unit
- Annotations
- @inline()
-
final
def
update(name: String, value: Any): Unit
- Annotations
- @inline()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @throws( ... )
- def →[B](y: B): (SamRecord, B)