case class MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char]) extends Product with Serializable
Represents the mismatches and deletions present in a read that has been aligned to a reference genome. The MD tag can be used to reconstruct the reference that an aligned read overlaps.
- start
Start position of the alignment.
- matches
A list of the ranges over which the read has a perfect sequence match.
- mismatches
A map of all the locations where a base mismatched.
- deletions
A map of all locations where a base was deleted.
- Alphabetic
- By Inheritance
- MdTag
- Serializable
- Serializable
- Product
- Equals
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
-
new
MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char])
- start
Start position of the alignment.
- matches
A list of the ranges over which the read has a perfect sequence match.
- mismatches
A map of all the locations where a base mismatched.
- deletions
A map of all locations where a base was deleted.
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
canEqual(other: Any): Boolean
We can check equality against MdTags.
We can check equality against MdTags.
- other
Object to see if we can compare against.
- returns
Returns True if the object is an MdTag.
- Definition Classes
- MdTag → Equals
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
def
countOfMismatches: Int
Returns the number of mismatches against the reference.
Returns the number of mismatches against the reference.
- returns
Number of mismatches against the reference
-
def
deletedBase(pos: Long): Option[Char]
Returns the base that was deleted at a position.
Returns the base that was deleted at a position.
- pos
Reference based position.
- returns
The base that was deleted at this position in the reference.
- val deletions: Map[Long, Char]
-
def
end(): Long
Returns the end position of the record described by this MD tag.
Returns the end position of the record described by this MD tag.
- returns
The reference based end position of this tag.
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(other: Any): Boolean
We implement equality checking by seeing whether two MD tags are at the same position and have the same value.
We implement equality checking by seeing whether two MD tags are at the same position and have the same value.
- other
An object to compare to.
- returns
True if the object is an MD tag at the same position and with the same string value. Else, false.
- Definition Classes
- MdTag → Equals → AnyRef → Any
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
getReference(read: RichAlignment, withGaps: Boolean = false): String
Given a read, returns the reference.
Given a read, returns the reference.
- read
A read for which one desires the reference sequence.
- withGaps
If true, applies INDEL gaps to the reference. Else, returns the raw reference sequence.
- returns
A string corresponding to the reference overlapping this read.
-
def
hasMismatches: Boolean
Returns whether this read has any mismatches against the reference.
Returns whether this read has any mismatches against the reference.
- returns
True if this read has mismatches. We do not return true if the read has no mismatches but has deletions.
-
def
hashCode(): Int
- returns
We implement hashing by hashing the string representation of the MD tag.
- Definition Classes
- MdTag → AnyRef → Any
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
isMatch(pos: ReferencePosition): Boolean
Returns whether a base is a match against the reference.
Returns whether a base is a match against the reference.
- pos
ReferencePosition object describing where to check.
- returns
True if base matches reference. False means that the base may be either a mismatch or a deletion.
-
def
isMatch(pos: Long): Boolean
Returns whether a base is a match against the reference.
Returns whether a base is a match against the reference.
- pos
Reference based position to check.
- returns
True if base matches reference. False means that the base may be either a mismatch or a deletion.
- val matches: List[NumericRange[Long]]
-
def
mismatchedBase(pos: Long): Option[Char]
Returns the mismatched base at a position.
Returns the mismatched base at a position.
- pos
Reference based position.
- returns
The base at this position in the reference.
- val mismatches: Map[Long, Char]
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
- val start: Long
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
Converts an MdTag object to a properly formatted MD string.
Converts an MdTag object to a properly formatted MD string.
- returns
MD string corresponding to [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)
- Definition Classes
- MdTag → AnyRef → Any
- See also
http://zenfractal.com/2013/06/19/playing-with-matches/
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
- Deprecated
(Since version ) see corresponding Javadoc for more information.