Multi-Container to store contigs, reads and a multiple alignment between them.
FragmentStore<TSpec[, TConfig]>
The specializing type.
Default: void
The configuration struct.
Default: FragmentStoreConfig<TSpec>
TAlignedReadStoreType of the alignedReadStore member.
TAlignedReadTagStoreType of the alignedReadTagStore member.
TAlignQualityStoreType of the alignQualityStore member.
TAnnotationNameStoreType of the annotationNameStore member.
TAnnotationStoreType of the annotationStore member.
TContigFileStoreType of the contigFileStore member.
TContigNameStoreType of the contigNameStore member.
TContigStoreType of the contigStore member.
TLibraryNameStoreType of the libraryNameStore member.
TLibraryStoreType of the libraryStore member.
TMatePairNameStoreType of the matePairNameStore member.
TMatePairStoreType of the matePairStore member.
TReadNameStoreType of the readNameStore member.
TReadSeqStoreType of the readSeqStore member.
TReadStoreType of the readStore member.
Data Members
alignedReadStoreString that stores <alignId, readId, contigId, pairMatchId, beginPos, endPos, gaps>.
alignedReadTagStoreString that maps from alignId to alignTag.
alignQualityStoreString that maps from alignId to <pairScore, score, errors>.
annotationNameStoreString that maps from annoId to annoName.
annotationStoreString that maps from annoId to <contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values>.
contigFileStoreString that maps from contigFileId to <fileName, firstContigId>.
contigNameStoreString that maps from contigId to contigName.
contigStoreString that maps from contigId to <contigSeq, contigGaps, contigFileId>.
libraryNameStoreString that maps from libId to libName.
libraryStoreString that maps from libId to <mean, std>.
matePairNameStoreString that maps from contigId to contigName.
matePairStoreString that maps from matePairId to <readId[2], libId>.
readNameStoreString that maps from readId to readName.
readSeqStoreString 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.
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.
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.
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.
SeqAn - Sequence Analysis Library -

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