FragmentStore

Class

FragmentStore

Multi container to store contigs, reads, multiple read alignments and genome annotations.

The FragmentStore is a data structure specifically designed for read mapping, genome assembly or gene annotation. These tasks typically require lots of data structures that are related to each other like: reads, mate-pairs, reference genome; pairwise alignments; genome annotation.

The FragmentStore subsumes all these data structures in an easy to use interface. It represents a multiple alignment of millions of reads or mate-pairs against a reference genome consisting of multiple contigs. Additionally, regions of the reference genome can be annotated with features like 'gene', 'mRNA', 'exon', 'intro' or custom features. The FragmentStore supports I/O functions to read/write a read alignment in Sam or Amos format and to read/write annotations in Gff/Gtf format.

The FragmentStore can be compared with a database where each table (called "store") is implemented as a String member of the FragmentStore class. The rows of each table (implemented as structs) are referred by their ids which are their positions in the string and not stored explicitly. The only exception is the alignedReadStore whose elements of type AlignedReadStoreElement contain an id-member as they may be rearranged in arbitrary order, e.g. by increasing genomic positions or by readId. Many stores have an associated name store to store element names. Each name store is a StringSet that stores the element name at the position of its id. All stores are present in the FragmentStore and empty if unused. The concrete types, e.g. the position types or read/contig alphabet, can be easily changed by defining a custom config struct which is a template parameter of the FragmentStore class.

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.
clearContigs	Removes all contigs from a fragment store.
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.
writeContigs	Write contigs from fragment store into file.

Examples

Load read alignments and a reference genome and display the multiple alignment in a genomic range:

File "store_example.cpp"

1	#include <iostream>
2	#include <seqan/store.h>
3
4	using namespace seqan;
5
6	int main ()
7	{
8	// instantiate emtpy FragmentStore and set file paths
9	FragmentStore<> store;
10	std::string pathGenome = std::string(SEQAN_PATH_TO_ROOT()) + "/core/demos/tutorial/store/ex1.fa";
11	std::string pathSAM = std::string(SEQAN_PATH_TO_ROOT()) + "/core/demos/tutorial/store/ex1.sam";
12
13	// load example genome and example reads and alignments
14	loadContigs(store, pathGenome.c_str());
15	std::ifstream file(pathSAM.c_str());
16	read(file, store, Sam());
17
18	// compute staircase read layout and print from position 30..129
19	AlignedReadLayout layout;
20	layoutAlignment(layout, store);
21	printAlignment(std::cout, Raw(), layout, store, 1, 30, 130, 0, 36);
22
23	return 0;
24	}

The staircase alignment looks as follows:

ATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
ATTTAA  AATTACAAAATATAGTTGAAAGCTCTAACAATAGA   AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA  AGTCTCTTATGAATTAA
ATTTA GAAATTACAAAATATAGTTGAAAGCTCTAACAATA ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG AGACAAGTCTCTTATGAATTAA
attta GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG    AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA  AGTCTCTTATGAATTAA
ATTTAA   ATTACAAAATATAGTTGAAAGATCTAACAATAGAC    CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA     TTATGAATTAA
ATTTAAGAA TTACAAAATATAGTTGAAAGCTCTAACAATAGACT     AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG     TATGAATTAA
ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA     GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC    ATGAATTAA
ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA      CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT    TGAATTAA
ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA      CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT    TGAATTAA
ATTTAAGAAATT CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA       GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT   GAATTAA
ATTTAAGAAAT   AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC       AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT  GAATTAA
ATTTAAGAAAT   AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC       AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT   AATTAA
ATTTAAGAAAT    AAATATAGTTGAAAGCTCTAACAATAGACTAAACC        GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG
ATTTAAGAAATT   AAATATAGTTGAAAGCTCTAACAATAGACTAAACC          AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
ATTTAAGAAATT    AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA        AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
ATTTAAGAAATTACA  ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA          GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
ATTTAAGAAATTACAA   ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC        GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
ATTTAAGAAATTACAAAATA AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG       AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT
ATTTAAGAAATTACAAAATAT  TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA      GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
ATTTAAGAAATTACAAAATATA   GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG TTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
ATTTAAGAAATTACAAAATATAGTTGAA    CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT      CTTGAAGACAAGTCTCTTATGAATTAA
ATTTAAGAAATTACAAAATATAGTTGAAA   CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT      TTGAAGACAAGTCTCTTATGAATTAA
ATTTAAGAAATTACAAAATATAGTTGAAAG   TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT       TGAAGACAAGTCTCTTATGAATTAA
ATTTAAGAAATTACAAAATATAGTTGAAAGCTCT ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA     TGAAGACAAGTCTCTTATGAATTAA
  TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC    GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT AAGACAAGTCTCTTATGAATTAA
   TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA                     GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
          TTACAAAATATAGTTGAAAGCTCTAACAATAGACT                   GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
                   ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC           GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
                          AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA      TCAGAACTTGAAGACAAGTCTCTTATGAATTAA
                          AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA               NAAGACAAGTCTCTTATGAATTAA
                           AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA              GAAGACAAGTCTCTTATGAATTAA
                                 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT               AGTCTCTTATGAATTAA
                                 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT                GTCTCTTATGAATTAA
                                  AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
                                  AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
                                     AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
                                     AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA

The following figures visualize the relations between the different stores:

Stores that are involved in the representation of a multiple read alignment.

Stores that are involved in the representation of a genome alignment.

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