Multi-Container to store contigs, reads and a multiple alignment between them.
FragmentStore<TSpec[, TConfig]>
Include Headers
The specializing type.
Default: void
The configuration struct.
Default: FragmentStoreConfig<TSpec>
Data Members
alignedReadStoreString that stores <alignId, readId, contigId, pairMatchId, beginPos, endPos, gaps>.
alignedReadTagStoreStringSet that maps from alignId to alignTag.
alignQualityStoreString that maps from alignId to <pairScore, score, errors>.
annotationKeyStoreStringSet that maps from keyId to the name of a key. The keyId is used to address values of an annotation.
annotationNameStoreStringSet that maps from annoId to annoName.
annotationStoreString that maps from annoId to <contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values>.
annotationTypeStoreStringSet that maps from typeId to the type name of an annotation, e.g. "gene" or "exon". typeId is a member of the AnnotationStoreElement.
contigFileStoreString that maps from contigFileId to <fileName, firstContigId>.
contigNameStoreStringSet that maps from contigId to contigName.
contigStoreString that maps from contigId to <contigSeq, contigGaps, contigFileId>.
libraryNameStoreStringSet that maps from libId to libName.
libraryStoreString that maps from libId to <mean, std>.
matePairNameStoreStringSet that maps from contigId to contigName.
matePairStoreString that maps from matePairId to <readId[2], libId>.
readNameStoreStringSet that maps from readId to readName.
readSeqStoreStringSet that maps from readId to readSeq.
readStoreString that maps from readId to <matePairId>.
appendAlignedReadAppends an aligned read entry to a fragment store.
appendMatePairAppends two paired-end reads to a fragment store.
appendReadAppends a read to a fragment store.
beginThe begin of a container.
calculateInsertSizesCalculates a string with insert sizes for each pair match.
calculateMateIndicesCalculates a string that maps the readId of a read to the readId of its mate.
clearContigsRemoves all contigs from a fragment store.
clearReadsRemoves all reads from a fragment store.
compactAlignedReadsRemoves invalid aligned reads and rename alignId sequentially beginning with 0.
compactPairMatchIdsRenames pairMatchId sequentially beginning with 0.
convertMatchesToGlobalAlignmentConverts all matches to a multiple global alignment in gap-space.
convertPairWiseToGlobalAlignmentConverts pair-wise alignments to a multiple global alignment.
endThe end of a container.
getClrRangeGet the "clear" range of a read alignment.
getMateNoReturns the mate number of read for a given readId.
getReadReturns the read with the given readId.
layoutAlignmentCalculates a visible layout of aligned reads.
loadContigManually loads a contig sequence.
loadContigsLoads contigs into fragment store.
loadReadsLoads reads into fragment store.
lockContigLocks a contig sequence from being removed.
lockContigsLocks all contig sequences from being removed.
printAlignmentPrints a window of the visible layout of reads into a outstream.
readLoads records from a file.
unlockAndFreeContigRemoves a previous contig lock and clears sequence no further lock exist.
unlockAndFreeContigsRemoves a previous lock for all contigs and clears sequences without lock.
unlockContigRemoves a previous contig lock.
unlockContigsRemoves a previous lock for all contigs.
writeSaves records to a file.
writeContigsWrite contigs from fragment store into file.
Stores that are involved in the representation of a multiple read alignment.
Stores that are involved in the representation of a genome alignment.
SeqAn - Sequence Analysis Library -

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