FragmentStore

Class

FragmentStore

Multi-Container to store contigs, reads and a multiple alignment between them.

FragmentStore<>

FragmentStore<TSpec[, TConfig]>

Include Headers

seqan/store.h

Parameters

TSpec	The specializing type. Default: void
TConfig	The configuration struct. Default: FragmentStoreConfig<TSpec>

Typedefs

TAlignedReadStore	Type of the alignedReadStore member.
TAlignedReadTagStore	Type of the alignedReadTagStore member.
TAlignQualityStore	Type of the alignQualityStore member.
TAnnotationKeyStore	Type of the annotationKeyStore member.
TAnnotationNameStore	Type of the annotationNameStore member.
TAnnotationStore	Type of the annotationStore member.
TAnnotationTypeStore	Type of the annotationTypeStore member.
TContigFileStore	Type of the contigFileStore member.
TContigNameStore	Type of the contigNameStore member.
TContigStore	Type of the contigStore member.
TLibraryNameStore	Type of the libraryNameStore member.
TLibraryStore	Type of the libraryStore member.
TMatePairNameStore	Type of the matePairNameStore member.
TMatePairStore	Type of the matePairStore member.
TReadNameStore	Type of the readNameStore member.
TReadSeqStore	Type of the readSeqStore member.
TReadStore	Type of the readStore member.

Data Members

alignedReadStore	String that stores <alignId, readId, contigId, pairMatchId, beginPos, endPos, gaps>.
alignedReadTagStore	StringSet that maps from alignId to alignTag.
alignQualityStore	String that maps from alignId to <pairScore, score, errors>.
annotationKeyStore	StringSet that maps from keyId to the name of a key. The keyId is used to address values of an annotation.
annotationNameStore	StringSet that maps from annoId to annoName.
annotationStore	String that maps from annoId to <contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values>.
annotationTypeStore	StringSet that maps from typeId to the type name of an annotation, e.g. "gene" or "exon". typeId is a member of the AnnotationStoreElement.
contigFileStore	String that maps from contigFileId to <fileName, firstContigId>.
contigNameStore	StringSet that maps from contigId to contigName.
contigStore	String that maps from contigId to <contigSeq, contigGaps, contigFileId>.
libraryNameStore	StringSet that maps from libId to libName.
libraryStore	String that maps from libId to <mean, std>.
matePairNameStore	StringSet that maps from contigId to contigName.
matePairStore	String that maps from matePairId to <readId[2], libId>.
readNameStore	StringSet that maps from readId to readName.
readSeqStore	StringSet that maps from readId to readSeq.
readStore	String that maps from readId to <matePairId>.

Functions

appendAlignedRead	Appends an aligned read entry to a fragment store.
appendMatePair	Appends two paired-end reads to a fragment store.
appendRead	Appends a read to a fragment store.
begin	The begin of a container.
calculateInsertSizes	Calculates a string with insert sizes for each pair match.
calculateMateIndices	Calculates a string that maps the readId of a read to the readId of its mate.
clearReads	Removes all reads from a fragment store.
compactAlignedReads	Removes invalid aligned reads and rename alignId sequentially beginning with 0.
compactPairMatchIds	Renames pairMatchId sequentially beginning with 0.
convertMatchesToGlobalAlignment	Converts all matches to a multiple global alignment in gap-space.
convertPairWiseToGlobalAlignment	Converts pair-wise alignments to a multiple global alignment.
end	The end of a container.
getClrRange	Get the "clear" range of a read alignment.
getMateNo	Returns the mate number of read for a given readId.
getRead	Returns the read with the given readId.
layoutAlignment	Calculates a visible layout of aligned reads.
loadContig	Manually loads a contig sequence.
loadContigs	Loads contigs into fragment store.
loadReads	Loads reads into fragment store.
lockContig	Locks a contig sequence from being removed.
lockContigs	Locks all contig sequences from being removed.
printAlignment	Prints a window of the visible layout of reads into a outstream.
read	Loads records from a file.
unlockAndFreeContig	Removes a previous contig lock and clears sequence no further lock exist.
unlockAndFreeContigs	Removes a previous lock for all contigs and clears sequences without lock.
unlockContig	Removes a previous contig lock.
unlockContigs	Removes a previous lock for all contigs.
write	Saves records to a file. Writes the basic information about the ArgParseOption to the provided stream.
writeContigs	Write contigs from fragment store into file.

Examples

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 - www.seqan.de