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finishm
(0.0.9)
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Documentation for finishm (0.0.9)
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README
Namespace Listing A-Z
A
ABVisualiser
(Bio::Assembly)
AcyclicConnectionFinder
(Bio::AssemblyGraphAlgorithms)
AllOrfsFinder
(Bio::AssemblyGraphAlgorithms)
AllProblemTrailsFinder
(Bio::AssemblyGraphAlgorithms::AllOrfsFinder)
AnchoredConnection
(Bio::AssemblyGraphAlgorithms::ContigPrinter)
AnyPriorityQueue
(DS)
Assembler
(Bio::FinishM)
Assembly
(Bio)
AssemblyGraphAlgorithms
(Bio)
B
BadFormatWriter
(Bio::FinishM)
BamProbeReadSelector
(Bio::AssemblyGraphAlgorithms)
Bio
Bubble
(Bio::AssemblyGraphAlgorithms::BubblyAssembler)
BubblyAssembler
(Bio::AssemblyGraphAlgorithms)
C
CProbeNodeFinder
(Bio::FinishM)
Checker
(Bio::FinishM::Primers)
CircuitousPathDetected
(Bio::AssemblyGraphAlgorithms::BubblyAssembler)
ComparableArray
(Bio::AssemblyGraphAlgorithms::BubblyAssembler)
Connection
(Bio::FinishM::ConnectionInterpreter)
ConnectionInterpreter
(Bio::FinishM)
ConnectivityBasedGraphFilter
(Bio::AssemblyGraphAlgorithms)
ContigPrinter
(Bio::AssemblyGraphAlgorithms)
CoverageBasedGraphFilter
(Bio::AssemblyGraphAlgorithms)
CycleCounter
(Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder)
CyclePath
(Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode)
CyclicTraversalNode
(Bio::AssemblyGraphAlgorithms::HeightFinder)
D
Dijkstra
(Bio::AssemblyGraphAlgorithms)
DistancedOrientedNode
(Bio::AssemblyGraphAlgorithms::Dijkstra)
DistancedOrientedNodeSet
(Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer)
DistancedOrientedNodeTrail
(Bio::AssemblyGraphAlgorithms::SequenceHasher)
DualStack
(Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder)
DynamicProgrammingProblem
(Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder)
DynamicProgrammingProblem
(Bio::AssemblyGraphAlgorithms::BubblyAssembler)
E
ExplorationPath
(Bio::AssemblyGraphAlgorithms::GraphExplorer)
Explorer
(Bio::FinishM)
F
FinishM
(Bio)
Finisher
(Bio::FinishM)
Fluff
(Bio::FinishM)
Fluffer
(Bio::AssemblyGraphAlgorithms)
FlufferHalfResult
(Bio::AssemblyGraphAlgorithms::Fluffer)
FlufferPathSet
(Bio::AssemblyGraphAlgorithms::Fluffer)
G
Gap
(Bio::FinishM::ScaffoldBreaker)
GapFiller
(Bio::FinishM)
Graph
(Bio::Velvet)
GraphExplorer
(Bio::AssemblyGraphAlgorithms)
GraphGenerator
(Bio::FinishM)
GraphWalkingException
(Bio::AssemblyGraphAlgorithms)
H
HeightFinder
(Bio::AssemblyGraphAlgorithms)
HybridGraph
(Bio::FinishM)
I
IllDefinedTrailDefinition
(Bio::Velvet::Graph::OrientedNodeTrail)
InputGenome
(Bio::FinishM)
InsufficientLengthException
(Bio::Velvet::Graph::OrientedNodeTrail)
InterestingPlace
(Bio::FinishM::Explorer)
K
KmerAbundancePattern
KmerCoverageBasedPathFilter
(Bio::AssemblyGraphAlgorithms)
KmerMultipleAbundanceHash
(Bio)
L
LazyGraphWalker
(Bio::AssemblyGraphAlgorithms)
LazyShortReadArray
(Bio::FinishM::HybridGraph)
Logging
(Bio::FinishM)
M
Marker
(Bio::AssemblyGraphAlgorithms::AllOrfsFinder)
MaxDistancedOrientedNode
(Bio::AssemblyGraphAlgorithms::SingleEndedAssembler)
MetaPath
(Bio::AssemblyGraphAlgorithms::BubblyAssembler)
N
Neighbour
(Bio::FinishM::PairedEndNeighbourFinder)
Node
(Bio::Velvet::Graph)
NodeArray
(Bio::FinishM::HybridGraph)
NodeFinder
(Bio::AssemblyGraphAlgorithms)
NodedRead
(Bio::Velvet::Graph)
NumberedProbe
O
ORFsFinder
(Bio::FinishM)
ORFsResult
(Bio::AssemblyGraphAlgorithms::AllOrfsFinder)
ORFsTracingTrail
(Bio::AssemblyGraphAlgorithms::AllOrfsFinder)
Oligo
(OligoDesigner)
OligoDesigner
OrientedNode
(Bio::Velvet::Graph::OrientedNodeTrail)
OrientedNodeTrail
(Bio::Velvet::Graph)
P
PairedEndAssembler
(Bio::AssemblyGraphAlgorithms)
PairedEndNeighbourFinder
(Bio::FinishM)
Path
(Bio::Assembly::ABVisualiser::SimplifiedGraph)
PathCounter
(Bio::FinishM)
PathSteppingStone
(Bio::FinishM::Sequence)
PossiblyCircularArray
(Bio::FinishM::ConnectionInterpreter)
PrimerList
(Bio::FinishM::Primers)
Primers
(Bio::FinishM)
PrintableConnection
(Bio::AssemblyGraphAlgorithms::ContigPrinter)
Probe
(Bio::FinishM::ConnectionInterpreter)
ProbedGraph
(Bio::FinishM)
ProblemSet
(Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder)
ProblemTrailFinder
(Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder)
R
ReadIdNodeIdStruct
(Bio::FinishM::VelvetCBinding)
ReadIdToNodeIdIndexationStruct
(Bio::FinishM::VelvetCBinding)
ReadIdToNodeIdLookupTableStruct
(Bio::FinishM::VelvetCBinding)
ReadInput
(Bio::FinishM)
ReadToNode
(Bio::FinishM)
RoundUp
(Bio::FinishM)
S
Scaffold
(Bio::FinishM::ScaffoldBreaker)
Scaffold
(Bio::FinishM::ConnectionInterpreter)
ScaffoldBreaker
(Bio::FinishM)
SearchResult
(Bio::AssemblyGraphAlgorithms::AllOrfsFinder)
Sequence
(Bio::FinishM)
SequenceHasher
(Bio::AssemblyGraphAlgorithms)
SimplifiedGraph
(Bio::Assembly::ABVisualiser)
SingleCoherentPathsBetweenNodesFinder
(Bio::AssemblyGraphAlgorithms)
SingleCoherentWanderer
(Bio::AssemblyGraphAlgorithms)
SingleEndedAssembler
(Bio::AssemblyGraphAlgorithms)
T
TrailSet
(Bio::AssemblyGraphAlgorithms)
TraversalNode
(Bio::AssemblyGraphAlgorithms::HeightFinder)
U
UnscaffoldedContig
(Bio::FinishM::ScaffoldBreaker)
UnscaffoldedContig
(Bio::FinishM::ConnectionInterpreter)
V
Variant
(Bio::AssemblyGraphAlgorithms::ContigPrinter)
Velvet
(Bio)
VelvetCBinding
(Bio::FinishM)
Visualise
(Bio::FinishM)
W
Wanderer
(Bio::FinishM)