class VanillaUmiConsensusCaller extends UmiConsensusCaller[VanillaConsensusRead] with LazyLogging
Calls consensus reads by grouping consecutive reads with the same SAM tag.
Consecutive reads with the SAM tag are partitioned into fragments, first of pair, and second of pair reads, and a consensus read is created for each partition. A consensus read for a given partition may not be returned if any of the conditions are not met (ex. minimum number of reads, minimum mean consensus base quality, ...).
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Instance Constructors
- new VanillaUmiConsensusCaller(readNamePrefix: String, readGroupId: String = "A", options: VanillaUmiConsensusCallerOptions = ..., rejects: Option[SAMFileWriter] = None)
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to any2stringadd[VanillaUmiConsensusCaller] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (VanillaUmiConsensusCaller, B)
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to ArrowAssoc[VanillaUmiConsensusCaller] 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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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- protected[java.lang]
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- @throws( ... )
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def
consensusFromSamRecords(records: Seq[SAMRecord]): Option[VanillaConsensusRead]
Creates a consensus read from the given records.
Creates a consensus read from the given records. If no consensus read was created, None is returned.
- Attributes
- protected[com.fulcrumgenomics.umi]
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def
consensusReadLength(reads: Seq[SourceRead], minReads: Int): Int
Calculates the length of the consensus read that should be produced.
Calculates the length of the consensus read that should be produced. The length is calculated as the maximum length at which minReads reads still have bases.
- reads
the set of reads being fed into the consensus
- minReads
the minimum number of reads required
- returns
the length of consensus read that should be created
- Attributes
- protected
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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 SAMRecords for a single source molecule and produces consensus records.
Takes in all the SAMRecords for a single source molecule and produces consensus 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
- VanillaUmiConsensusCaller → UmiConsensusCaller
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def
createSamRecord(read: VanillaConsensusRead, readType: ReadType): SAMRecord
Creates a
SAMRecordfrom the called consensus base and qualities.Creates a
SAMRecordfrom the called consensus base and qualities.- Attributes
- protected
- Definition Classes
- VanillaUmiConsensusCaller → UmiConsensusCaller
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def
ensuring(cond: (VanillaUmiConsensusCaller) ⇒ Boolean, msg: ⇒ Any): VanillaUmiConsensusCaller
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to Ensuring[VanillaUmiConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (VanillaUmiConsensusCaller) ⇒ Boolean): VanillaUmiConsensusCaller
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to Ensuring[VanillaUmiConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): VanillaUmiConsensusCaller
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to Ensuring[VanillaUmiConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): VanillaUmiConsensusCaller
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to Ensuring[VanillaUmiConsensusCaller] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
filterToMostCommonAlignment(recs: Seq[SAMRecord]): Seq[SAMRecord]
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[com.fulcrumgenomics.umi]
- Definition Classes
- UmiConsensusCaller
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def
finalize(): Unit
- Attributes
- protected[java.lang]
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- @throws( classOf[java.lang.Throwable] )
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to StringFormat[VanillaUmiConsensusCaller] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
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def
hashCode(): Int
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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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
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
- AnyRef
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val options: VanillaUmiConsensusCallerOptions
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val
readGroupId: String
- Definition Classes
- VanillaUmiConsensusCaller → UmiConsensusCaller
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val
readNamePrefix: String
- Definition Classes
- VanillaUmiConsensusCaller → 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
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def
rejectRecords(recs: Traversable[SAMRecord]): Unit
If a reject writer was provided, emit the reads to that writer.
If a reject writer was provided, emit the reads to that writer.
- Attributes
- protected
- Definition Classes
- VanillaUmiConsensusCaller → UmiConsensusCaller
- val rejects: Option[SAMFileWriter]
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def
sourceMoleculeId(rec: SAMRecord): String
Returns the value of the SAM tag directly.
Returns the value of the SAM tag directly.
- rec
a SAMRecord
- returns
an identified for the source molecule
- Definition Classes
- VanillaUmiConsensusCaller → UmiConsensusCaller
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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. The default method is to use the SAM flag to find unpaired reads, first of pair reads, and second of pair reads.
- Attributes
- protected
- Definition Classes
- UmiConsensusCaller
-
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
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def
toSourceRead(rec: SAMRecord, minBaseQuality: PhredScore): 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[com.fulcrumgenomics.umi]
- Definition Classes
- UmiConsensusCaller
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def
toString(): String
- Definition Classes
- AnyRef → Any
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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
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final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... )
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def
→[B](y: B): (VanillaUmiConsensusCaller, B)
- Implicit
- This member is added by an implicit conversion from VanillaUmiConsensusCaller to ArrowAssoc[VanillaUmiConsensusCaller] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc