Class
FragmentStore
Multi-Container to store contigs, reads and a multiple alignment between them.
FragmentStore<>
FragmentStore<TSpec[, TConfig]>
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.
TAnnotationNameStore | Type of the annotationNameStore member.
TAnnotationStore | Type of the annotationStore 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 | String that maps from alignId to alignTag.
alignQualityStore | String that maps from alignId to <pairScore, score, errors>.
annotationNameStore | String that maps from annoId to annoName.
annotationStore | String that maps from annoId to <contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values>.
contigFileStore | String that maps from contigFileId to <fileName, firstContigId>.
contigNameStore | String that maps from contigId to contigName.
contigStore | String that maps from contigId to <contigSeq, contigGaps, contigFileId>.
libraryNameStore | String that maps from libId to libName.
libraryStore | String that maps from libId to <mean, std>.
matePairNameStore | String that maps from contigId to contigName.
matePairStore | String that maps from matePairId to <readId[2], libId>.
readNameStore | String that maps from readId to readName.
readSeqStore | String 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.
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.
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.
writeContigs | Write contigs from fragment store into file.

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Page built @2012/03/14 16:34:45