Index

_

__init__() (shasta.Assembler method)

A

accessAlignmentCandidates() (shasta.Assembler method) accessAlignmentCandidateTable() (shasta.Assembler method) accessAlignmentData() (shasta.Assembler method) accessAlignmentDataReadWrite() (shasta.Assembler method) accessAssemblyGraphEdgeLists() (shasta.Assembler method) accessAssemblyGraphEdges() (shasta.Assembler method) accessAssemblyGraphOrientedReadsByEdge() (shasta.Assembler method) accessAssemblyGraphSequences() (shasta.Assembler method) accessAssemblyGraphVertices() (shasta.Assembler method) accessCompressedAlignments() (shasta.Assembler method) accessKmers() (shasta.Assembler method) accessMarkerGraphConsensus() (shasta.Assembler method) accessMarkerGraphCoverageData() (shasta.Assembler method) accessMarkerGraphEdges() (shasta.Assembler method) accessMarkerGraphReverseComplementEdge() (shasta.Assembler method) accessMarkerGraphReverseComplementVertex() (shasta.Assembler method) accessMarkerGraphVertexRepeatCounts() (shasta.Assembler method) accessMarkerGraphVertices() (shasta.Assembler method)

accessMarkers() (shasta.Assembler method) accessReadGraph() (shasta.Assembler method) accessReadGraphReadWrite() (shasta.Assembler method) accessSortedMarkers() (shasta.Assembler method) alignOrientedReads() (shasta.Assembler method) alignOrientedReads1() (shasta.Assembler method) alignOrientedReads4() (shasta.Assembler method) alignOverlappingOrientedReads() (shasta.Assembler method) alignPseudoPaths() (shasta.Assembler method) analyzeAlignmentMatrix() (shasta.Assembler method) analyzeAssemblyGraphBubbles() (shasta.Assembler method) analyzeMarkerGraphForks() (shasta.Assembler method) analyzeReadGraph() (shasta.Assembler method) assemble() (shasta.Assembler method) assembleAssemblyGraphEdge() (shasta.Assembler method) assembleMarkerGraphEdges() (shasta.Assembler method) assembleMarkerGraphVertices() (shasta.Assembler method) Assembler (class in shasta)

C

checkMarkerGraphIsStrandSymmetric() (shasta.Assembler method) cleanupDuplicateMarkers() (shasta.Assembler method) colorCompressedAssemblyGraph() (shasta.Assembler method) colorGfaBySimilarityToSegment() (shasta.Assembler method) colorGfaKeySegments() (shasta.Assembler method) colorGfaWithTwoReads() (shasta.Assembler method) computeAlignments() (shasta.Assembler method) computeAssemblyStatistics() (shasta.Assembler method) computeMarkerGraphCoverageHistogram() (shasta.Assembler method) computeMarkerGraphVerticesCoverageData() (shasta.Assembler method) computeReadGraphConnectedComponents() (shasta.Assembler method) computeSortedMarkers() (shasta.Assembler method)

createAssemblyGraph2() (shasta.Assembler method) createAssemblyGraphEdges() (shasta.Assembler method) createAssemblyGraphVertices() (shasta.Assembler method) createCompressedAssemblyGraph() (shasta.Assembler method) createMarkerGraphEdges() (shasta.Assembler method) createMarkerGraphEdgesStrict() (shasta.Assembler method) createMarkerGraphSecondaryEdges() (shasta.Assembler method) createMarkerGraphVertices() (shasta.Assembler method) createReadGraph() (shasta.Assembler method) createReadGraph2() (shasta.Assembler method) createReadGraphMode1() (shasta.Assembler method) createReadGraphUsingPseudoPaths() (shasta.Assembler method)

D

detangle() (shasta.Assembler method)

detangle2() (shasta.Assembler method)

F

findAlignmentCandidatesLowHash0() (shasta.Assembler method) findAlignmentCandidatesLowHash1() (shasta.Assembler method) findMarkerGraphReverseComplementEdges() (shasta.Assembler method) findMarkerGraphReverseComplementVertices() (shasta.Assembler method) findMarkers() (shasta.Assembler method)

flagChimericReads() (shasta.Assembler method) flagCrossStrandReadGraphEdges1() (shasta.Assembler method) flagCrossStrandReadGraphEdges2() (shasta.Assembler method) flagInconsistentAlignments() (shasta.Assembler method) flagPalindromicReads() (shasta.Assembler method)

G

gatherOrientedReadsByAssemblyGraphEdge() (shasta.Assembler method) getAlignmentCandidates() (shasta.Assembler method) getGlobalMarkerGraphVertex() (shasta.Assembler method)

getGlobalMarkerGraphVertexMarkers() (shasta.Assembler method) getMarkerGraphMinCoverageUsed() (shasta.Assembler method) getMarkers() (shasta.Assembler method) getReads() (shasta.Assembler method)

H

histogramReadLength() (shasta.Assembler method)

M

module shasta

P

pruneMarkerGraphStrongSubgraph() (shasta.Assembler method)

R

randomlySelectKmers() (shasta.Assembler method) readGraphClustering() (shasta.Assembler method) refineMarkerGraph() (shasta.Assembler method)

removeAssemblyGraph() (shasta.Assembler method) removeMarkerGraph() (shasta.Assembler method) removeReadGraphBridges() (shasta.Assembler method) reverseTransitiveReduction() (shasta.Assembler method)

S

selectKmers2() (shasta.Assembler method) selectKmers4() (shasta.Assembler method) selectKmersBasedOnFrequency() (shasta.Assembler method) setMarkerGraphEdgeFlags() (shasta.Assembler method)

setupConsensusCaller() (shasta.Assembler method) shasta module simplifyMarkerGraph() (shasta.Assembler method)

T

test() (shasta.Assembler method)

transitiveReduction() (shasta.Assembler method)

V

vertexCoverageStatisticsByKmerId() (shasta.Assembler method)

W

writeAlignmentCandidates() (shasta.Assembler method) writeAlignmentDetails() (shasta.Assembler method) writeAssemblyGraph() (shasta.Assembler method) writeBadMarkerGraphVertices() (shasta.Assembler method) writeFasta() (shasta.Assembler method) writeGfa1() (shasta.Assembler method) writeGfa1BothStrands() (shasta.Assembler method) writeKmers() (shasta.Assembler method) writeLocalAlignmentCandidateReads() (shasta.Assembler method)

writeLocalReadGraphReads() (shasta.Assembler method) writeMarkerFrequency() (shasta.Assembler method) writeMarkers() (shasta.Assembler method) writeOrientedReadPath() (shasta.Assembler method) writeOrientedReadsByAssemblyGraphEdge() (shasta.Assembler method) writeOverlappingReads() (shasta.Assembler method) writeParallelMarkerGraphEdges() (shasta.Assembler method) writePseudoPath() (shasta.Assembler method) writeReadGraphEdges() (shasta.Assembler method)