class DuplexConsensusCaller extends UmiConsensusCaller[DuplexConsensusRead] with LazyLogging
Creates duplex consensus reads from SamRecords that have been grouped by their source molecule but not yet by source strand.
Filters incoming bases by quality before building the duplex.
Output reads and bases are constructed only if there is at least one read from each source molecule strand. Otherwise no filtering is performed.
Note that a consequence of the above is that the output reads can be shorter than _some_ of the input reads if the input reads are of varying length; they will be the length at which there is coverage from both source strands.
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Instance Constructors
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new
DuplexConsensusCaller(readNamePrefix: String, readGroupId: String = "A", minInputBaseQuality: PhredScore = ..., trim: Boolean = false, errorRatePreUmi: PhredScore = ..., errorRatePostUmi: PhredScore = ..., minReads: Seq[Int] = Seq(1), maxReadsPerStrand: Int = ...)
- readNamePrefix
the prefix to apply to all consensus read names
- readGroupId
the read group ID to apply to all created consensus reads
- minInputBaseQuality
the minimum input base quality score to use a raw read's base
- trim
if true, quality trim reads in addition to masking. If false just mask.
- errorRatePreUmi
the estimated rate of errors in the DNA prior to attaching UMIs
- errorRatePostUmi
the estimated rate of errors in the DNA post attaching UMIs
- minReads
the minimum number of input reads to a consensus read (see CallDuplexConsensusReads).
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to any2stringadd[DuplexConsensusCaller] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (DuplexConsensusCaller, B)
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to ArrowAssoc[DuplexConsensusCaller] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
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- @inline()
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final
def
==(arg0: Any): Boolean
- Definition Classes
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val
NoCall: Byte
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
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val
NoCallQual: PhredScore
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
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def
addStatistics(caller: UmiConsensusCaller[DuplexConsensusRead]): Unit
Adds the given caller's statistics (counts) to this caller.
Adds the given caller's statistics (counts) to this caller.
- Definition Classes
- UmiConsensusCaller
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- protected[lang]
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def
consensusReadsConstructed: Long
Returns the number of consensus reads constructed by this caller.
Returns the number of consensus reads constructed by this caller.
- Definition Classes
- UmiConsensusCaller
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final
def
consensusReadsFromSamRecords(recs: Seq[SamRecord]): Seq[SamRecord]
Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.
Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.
- recs
the full set of source SamRecords for a source molecule
- returns
a seq of consensus SAM records, may be empty
- Definition Classes
- UmiConsensusCaller
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def
consensusSamRecordsFromSamRecords(recs: Seq[SamRecord]): Seq[SamRecord]
Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.
Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.
- recs
the full set of source SamRecords for a source molecule
- returns
a seq of consensus SAM records, may be empty
- Attributes
- protected
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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def
createSamRecord(read: DuplexConsensusRead, readType: ReadType, umis: Seq[String] = Seq.empty): SamRecord
Creates a SamRecord with a ton of additional tags annotating the duplex read.
Creates a SamRecord with a ton of additional tags annotating the duplex read.
- Attributes
- protected
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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def
emptyClone(): DuplexConsensusCaller
Returns a clone of this consensus caller in a state where no previous reads were processed.
Returns a clone of this consensus caller in a state where no previous reads were processed. I.e. all counters are set to zero.
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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def
ensuring(cond: (DuplexConsensusCaller) ⇒ Boolean, msg: ⇒ Any): DuplexConsensusCaller
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to Ensuring[DuplexConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (DuplexConsensusCaller) ⇒ Boolean): DuplexConsensusCaller
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to Ensuring[DuplexConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): DuplexConsensusCaller
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to Ensuring[DuplexConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): DuplexConsensusCaller
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to Ensuring[DuplexConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val errorRatePostUmi: PhredScore
- val errorRatePreUmi: PhredScore
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def
filterToMostCommonAlignment(recs: Seq[SourceRead]): Seq[SourceRead]
Takes in a non-empty seq of SamRecords and filters them such that the returned seq only contains those reads that share the most common alignment of the read sequence to the reference.
Takes in a non-empty seq of SamRecords and filters them such that the returned seq only contains those reads that share the most common alignment of the read sequence to the reference. If two or more different alignments share equal numbers of reads, the 'most common' will be an arbitrary pick amongst those alignments, and the group of reads with that alignment will be returned.
For the purposes of this method all that is implied by "same alignment" is that any insertions or deletions are at the same position and of the same length. This is done to allow for differential read length (either due to sequencing or untracked hard-clipping of adapters) and for differential soft-clipping at the starts and ends of reads.
NOTE: filtered out reads are sent to the rejectRecords method and do not need further handling
- Attributes
- protected[umi]
- Definition Classes
- UmiConsensusCaller
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def
finalize(): Unit
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to StringFormat[DuplexConsensusCaller] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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def
logStatistics(logger: Logger): Unit
Logs statistics about how many reads were seen, and how many were filtered/discarded due to various filters.
Logs statistics about how many reads were seen, and how many were filtered/discarded due to various filters.
- Definition Classes
- UmiConsensusCaller
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lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val maxReadsPerStrand: Int
- val minInputBaseQuality: PhredScore
- val minReads: Seq[Int]
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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val
readGroupId: String
A RG.ID to apply to all generated reads.
A RG.ID to apply to all generated reads.
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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val
readNamePrefix: String
A prefix to use on all read names.
A prefix to use on all read names. If None then a suitable prefix will be synthesized.
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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def
readsFilteredInsufficientSupport: Long
Returns the number of raw reads filtered out due to there being insufficient reads present to build the necessary set of consensus reads.
Returns the number of raw reads filtered out due to there being insufficient reads present to build the necessary set of consensus reads.
- Definition Classes
- UmiConsensusCaller
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def
readsFilteredMinorityAlignment: Long
Returns the number of raw reads filtered out because their alignment disagreed with the majority alignment of all raw reads for the same source molecule.
Returns the number of raw reads filtered out because their alignment disagreed with the majority alignment of all raw reads for the same source molecule.
- Definition Classes
- UmiConsensusCaller
-
def
rejectRecords(reason: String, rec: SamRecord*): Unit
Records that the supplied records were rejected, and not used to build a consensus read.
Records that the supplied records were rejected, and not used to build a consensus read.
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
-
def
rejectRecords(recs: Iterable[SamRecord], reason: String): Unit
Records that the supplied records were rejected, and not used to build a consensus read.
Records that the supplied records were rejected, and not used to build a consensus read.
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
-
def
sourceMoleculeId(rec: SamRecord): String
Returns the MI tag **minus** the trailing suffix that identifies /A vs /B
Returns the MI tag **minus** the trailing suffix that identifies /A vs /B
- rec
a SamRecord
- returns
an identified for the source molecule
- Attributes
- protected[umi]
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
-
def
subGroupRecords(records: Seq[SamRecord]): (Seq[SamRecord], Seq[SamRecord], Seq[SamRecord])
Split records into those that should make a single-end consensus read, first of pair consensus read, and second of pair consensus read, respectively.
Split records into those that should make a single-end consensus read, first of pair consensus read, and second of pair consensus read, respectively. This method is overridden in DuplexConsensusCaller to improve performance since no fragment reads should be given to this method.
- Attributes
- protected
- Definition Classes
- DuplexConsensusCaller → UmiConsensusCaller
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def
sum(ss: Array[Short]): Int
Sums a short array into an Int to avoid overflow.
Sums a short array into an Int to avoid overflow.
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toSourceRead(rec: SamRecord, minBaseQuality: PhredScore, trim: Boolean): Option[SourceRead]
Converts from a SamRecord into a SourceRead.
Converts from a SamRecord into a SourceRead. During conversion the record is end-trimmed to remove Ns and bases below the
minBaseQuality. Remaining bases that are belowminBaseQualityare then masked to Ns.- returns
Some(SourceRead) if there are any called bases with quality > minBaseQuality, else None
- Attributes
- protected[umi]
- Definition Classes
- UmiConsensusCaller
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
def
totalFiltered: Long
Returns the total number of reads filtered for any reason.
Returns the total number of reads filtered for any reason.
- Definition Classes
- UmiConsensusCaller
-
def
totalReads: Long
Returns the total number of input reads examined by the consensus caller so far.
Returns the total number of input reads examined by the consensus caller so far.
- Definition Classes
- UmiConsensusCaller
- val trim: Boolean
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... ) @native()
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def
→[B](y: B): (DuplexConsensusCaller, B)
- Implicit
- This member is added by an implicit conversion from DuplexConsensusCaller to ArrowAssoc[DuplexConsensusCaller] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc