FragmentStore - SeqAn API Documentation

# Class FragmentStore
Multi-container to store contigs, reads, multiple read alignments and genome annotations.

Defined in | <seqan/store.h>
Signature | `template <[typename TSpec[, typename TConfig]]> class FragmentStore;`

## Template Parameters

`TSpec` | The specialializing type. Default: `void`.
`TConfig` | The configuration struct. Default: `FragmentStoreConfig<TSpec>`.

## Member Function Overview

- `void clearReads(store);`
  Removes all reds from a FragmentStore.

## Interface Function Overview

- `TSize appendAlignedRead(store, readId, contigId, beginPos, endPos[, pairMatchId]);`
  Appends an aligned read entyr to a fragment store.
- `TSize appendMatePair(store, readSeq1, readSeq2[, name1, name2]);`
  Appends the two reads of a mate pair to a FragmentStore.
- `TSize appendRead(store, read[, matePairId]);, TSize appendRead(store, read, name[, matePairId]);`
  Append a read to a FragmentStore.
- `void calculateInsertSizes(insertSizes, store);`
  Calcualtes a string wtih insert sizes for each pair match.
- `void calculateMateIndices(mateIndices, store);`
  Calculates a string that maps the readId of a read to the index of its mate in the alignedReadStore.
- `void clearContigs(store);`
  REvmoes all contigs from a FragmentStore.
- `TSize compactAlignedReads(store);`
  Remove invalid aligned reads and rename the alignId's sequentially beginning with 0.
- `TSize compactPairMatchIds(store);`
  Renames pairMatchId sequentially beginning with 0.
- `void convertMatchesToGlobalAlignment(store, score, shrinkMatches);`
  Converts all matches to a multiple global alignment in gap-space.
- `void convertPairWiseToGlobalAlignment(store, pairwiseContigGaps);`
  Converts pairwise alignments to a multiple global alignment.
- `void getClrRange(store, alignEl, begClr, endClr);`
  Get the "clear" range of a read alignment.
- `int getMateNo(store, readId);`
  Returns the mate number for a read given a readId.
- `TRead getRead(store, id);`
  Returns the read with the given readId.
- `bool loadContig(store, contigId);`
  Manually load a contig sequence.
- `bool loadContigs(store, fileName[, loadSeqs]);, bool loadContigs(store, fileNameList[, loadSeqs]);`
  Load contigs into a FragmentStore.
- `bool loadReads(store, fileName);, bool loadReads(store, fileNameL, fileNameR);`
  Loads reads into FragmentStore
- `bool lockContig(store, contigId);`
  Locks a contig sequence from being removed.
- `bool lockContigs(store);`
  Locks all contig sequences from being remove.
- `int read(file, store, tag);`
  Read the contents of a FragmentStore from a file.
- `void readRecords(store, bamFileIn[, importFlags]);, void readRecords(store, gffFileIn);, void readRecords(store, ucscFileIn);`
  Read all records from a file.
- `bool unlockContig(store, contigId);`
  Removes a previous contig lock and clears the sequence if no further lock exists.
- `bool unlockAndFreeContigs(store);`
  Unlocks all contig sequences and clears sequences without lock.
- `bool unlockContig(store, contigId);`
  Removes a previous contig lock.
- `bool unlockContigs(store);`
  Unlocks all contig sequences.
- `int write(file, store, tag);`
  Write the contents of a FragmentStore to a file.
- `bool writeContigs(file, store, tag);`
  Write contigs from FragmentStore into a StreamConcept.
- `void writeRecords(bamFileOut, store);, void writeRecords(gffFileOut, store);, void writeRecords(ucscFileIn, store);`
  Write all records to a file.

## Member Typedef Overview

- `typedef (..) TFragmentStore::TAlignedReadStore;`
  Type of the alignedReadStore member.
- `typedef (..) TFragmentStore::TAlignedReadTagStore;`
  Type of the alignedReadTagStore member.
- `typedef (..) TFragmentStore::TAlignQualityStore;`
  Type of the alignQualityStore member.
- `typedef (..) TFragmentStore::TAnnotationKeyStore;`
  Type of the annotationKeyStore member.
- `typedef (..) TFragmentStore::TAnnotationNameStore;`
  Type of the annotationNameStore member.
- `typedef (..) TFragmentStore::TAnnotationStore;`
  Type of the annotationStore member.
- `typedef (..) TFragmentStore::TAnnotationTypeStore;`
  Type of the annotationTypeStore member.
- `typedef (..) TFragmentStore::TContigFileStore;`
  Type of the contigFileStore member.
- `typedef (..) TFragmentStore::TContigNameStore;`
  Type of the contigNameStore member.
- `typedef (..) TFragmentStore::TContigStore;`
  Type of the contigStore member.
- `typedef (..) TFragmentStore::TLibraryNameStore;`
  Type of the libraryNameStore member.
- `typedef (..) TFragmentStore::TMatePairNameStore;`
  Type of the matePairNameStore member.
- `typedef (..) TFragmentStore::TMatePairStore;`
  Type of the matePairStore member.
- `typedef (..) TFragmentStore::TReadNameStore;`
  Type of the readNameStore member.
- `typedef (..) TFragmentStore::TReadSeqStore;`
  Type of the readSeqStore member.
- `typedef (..) TFragmentStore::TReadStore;`
  Type of the readStore member.

## Member Variable Overview

- `FragmentStore::TAlignedReadStore FragmentStore::alignedReadStore`
  String that stores (alignId, readId, contigId, pairMatchId, beginPos, endPos, gapAnchors).
- `FragmentStore::TAlignedReadTagStore FragmentStore::alignedReadTagStore`
  StringSet that maps from alignId to alignTag.
- `FragmentStore::TAlignQualityStore FragmentStore::alignQualityStore`
  String that maps from alignId to (pairScore, score, errors).
- `FragmentStore::TAnnotationKeyStore FragmentStore::annotationKeyStore`
  StringSet that maps from keyId to the name of a key. The keyId is used to address values of an annotation.
- `FragmentStore::TAnnotationNameStore FragmentStore::annotationNameStore`
  StringSet that maps from annoId to annoName;
- `FragmentStore::TAnnotationStore FragmentStore::annotationStore`
  String that maps from annoId to (contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values).
- `FragmentStore::TAnnotationTypeStore FragmentStore::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.
- `FragmentStore::TContigFileStore FragmentStore::contigFileStore`
  String that maps from contigId to (contigSeq, contigGaps, contigFileId).
- `FragmentStore::TContigNameStore FragmentStore::contigNameStore`
  StringSet that maps from contigId to contigName.
- `FragmentStore::TContigStore FragmentStore::contigStore`
  String that maps from contigId to (contigSeq, contigGaps, contigFileId).
- `FragmentStore::TLibraryNameStore FragmentStore::libraryNameStore`
  A StringSet that maps from libId to libName.
- `FragmentStore::TLibraryStore FragmentStore::libraryStore`
  String that maps from libId to (mean, std).
- `FragmentStore::TContigNameStore FragmentStore::matePairNameStore`
  StringSet that maps from contigId to matePairName.
- `FragmentStore::TMatePairStore FragmentStore::matePairStore`
  String that maps from matePairId to (readId[2], libId).
- `FragmentStore::TReadNameStore FragmentStore::readNameStore`
  StringSet that maps from readId to readName.
- `FragmentStore::TReadSeqStore FragmentStore::readSeqStore`
  StringSet that maps from readId to readSeq.
- `FragmentStore::TReadStore FragmentStore::readStore`
  A String that maps from readId to matePairId.

## Detailed Description

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.

### Examples

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

    #include <iostream>
    #include <seqan/store.h>

    using namespace seqan;

    int main()
    {
        // instantiate emtpy FragmentStore and set file paths
        FragmentStore<> store;
        std::string pathGenome = getAbsolutePath("/demos/tutorial/store/ex1.fa");
        std::string pathSAM    = getAbsolutePath("/demos/tutorial/store/ex1.sam");

        // load example genome and example reads and alignments
        loadContigs(store, pathGenome.c_str());
        BamFileIn bamFile(pathSAM.c_str());
        readRecords(store, bamFile);

        // compute staircase read layout and print from position 30..129
        AlignedReadLayout layout;
        layoutAlignment(layout, store);
        printAlignment(std::cout, layout, store, 1, 30, 130, 0, 36);

        return 0;
    }

Demo: demos/dox/store/store_example.cpp

    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

### Remarks

The following figures visualize the relations between the different stores:

## Member Functions Detail

### `void clearReads(store);`

Removes all reds from a FragmentStore.

#### Parameters

`store` | The FragmentStore to remove all reads from.

Clears the readStore, readSeqStore, and readNameStore.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Interface Functions Detail

### `TSize appendAlignedRead(store, readId, contigId, beginPos, endPos[, pairMatchId]);`

Appends an aligned read entyr to a fragment store.

#### Parameters

`store` | The FragmentStore to append to.
`readId` | The id of the read to append an alignment for.
`contigId` | The id of the contig of the alignment.
`beginPos` | The begin position of the alignment.
`endPos` | The end position of the alignment.
`pairMatchId` | The id of the alignedRead pair. Default: `FragmentStore::INVALID_ID` which corresponds to an unmated read.

#### Returns

`TSize` | The alignedReadId of the alignment.

#### Remarks

This function appends a single read alignment to the alignedReadStore. Note that this really only adds a match. To generate a global alignment out of all these matches, use convertMatchesToGlobalAlignment.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- appendRead

### `TSize appendMatePair(store, readSeq1, readSeq2[, name1, name2]);`

Appends the two reads of a mate pair to a FragmentStore.

#### Parameters

`store` | The FragmentStore to append the mate pair to.
`readSeq1` | The read sequence of the first read.
`readSeq2` | The read sequence of the second read.
`name1` | The read name of the first read.
`name2` | The read name of the first read.

#### Returns

`TSize` | The matePairId of the newly appended mate pair. TSize is the size type of the matePairStore.

#### Remarks

This function appends two reads to the readStore and readSeqStore and a mate pair entry for both them to the matePairStore. If names are given, they are appended to readNameStore.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSize appendRead(store, read[, matePairId]); TSize appendRead(store, read, name[, matePairId]);`

Append a read to a FragmentStore.

#### Parameters

`store` | The FragmentStore to append the read to.
`read` | The read sequence. Type: ContainerConcept.
`name` | The name of the read. Type: CharString.
`matePairId` | ID of the mate-pair that this read is part of. Default: `FragmentStore::INVALID_ID` which corresponds to an unmated read.

#### Returns

`TSize` | The readId of the newly appended read. TSize is the size type of the readStore.

This funciton appends a single read to the readStore and readSeqStore.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### See Also

- getRead

### `void calculateInsertSizes(insertSizes, store);`

Calcualtes a string wtih insert sizes for each pair match.

#### Parameters

`insertSizes` | A String of insert sizes. This string is accordingly resized and can be addressed by the pairMatchId.
`store` | The FragmentStore to compute the insert sizes for.

#### Remarks

This function calls compactPairMatchIds first and calcualte the insert size for every pair match. The insert size of a pair match is the outer distance between the two matches.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void calculateMateIndices(mateIndices, store);`

Calculates a string that maps the readId of a read to the index of its mate in the alignedReadStore.

#### Parameters

`mateIndices` | A String with the resulting mate indices. This string is accordingly resized and can be addressed by the readId.
`store` | The FragmentStore.

Entries of reads without a mate contain `INVALID_ID`.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void clearContigs(store);`

REvmoes all contigs from a FragmentStore.

#### Parameters

`store` | The FragmentStore to remove all contigs from.

This function clears the contigStore and contigNameStore.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSize compactAlignedReads(store);`

Remove invalid aligned reads and rename the alignId's sequentially beginning with 0.

#### Parameters

`store` | The FragmentStore to compact the aligned reads of.

#### Returns

`s` | TSize The new size of the alignedReadStore. TSize is the size type of the alignedReadStore.

#### Remarks

This function removes all entries from the alignedReadStore whose alignId is equal to `INVALID_ID` as well as orphan entries in alignQualityStore. Afterwards, the alignIds are renamed sequentially beginning with 0. This function can be used to remove alignments which are flagged by previously setting their id to INVALID_ID.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSize compactPairMatchIds(store);`

Renames pairMatchId sequentially beginning with 0.

#### Parameters

`store` | The FragmentStore to compact pair match ids of.

#### Returns

`TSize` | The number of pair matches. TSize is the size type of alignedReadStore.

#### Remarks

This function renames the pairMatchId in the alignedReadStore sequentially beginning with 0. Two read alignments can be identified to be pair match if they have the same pairMatchId. Please note that paired reads not necessarily have to map as a pair match, e.g. if they are on different ocntigs or have the same orientation or a wrong insert size.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void convertMatchesToGlobalAlignment(store, score, shrinkMatches);`

Converts all matches to a multiple global alignment in gap-space.

#### Parameters

`store` | The fragment store. Types: FragmentStore
`score` | A score object used by globalAlignment in this function.
`shrinkMatches` | States whether the matches should be shrinked. Types: True, False

#### Remarks

Before calling this function all `gaps` structures in alignedReadStore and contigStore must be empty, i.e. there are no gaps in the alignments. This function iterates over entries in the alignedReadStore and semi-global aligns each read to its contig segments given by begin and end position. Gaps introduced by these pair-wise alignments are then inserted to the affected contig and reads correspondingly.

The invariant that positions in the alignedReadStore are in gap-space holds before (there were no gaps in alignments) and after calling this functions.

If the alignQualityStore of the FragmentStore is empty when `convertMatchesToGlobalAlignment()` is called then the alignQualityStore is filled with the edit distance scores.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void convertPairWiseToGlobalAlignment(store, pairwiseContigGaps);`

Converts pairwise alignments to a multiple global alignment.

#### Parameters

`store` | The fragment store. Types: FragmentStore
`pairwiseContigGaps` | A String of anchored contig gaps for every pairwise alignment.

#### Remarks

Before calling this function the `gaps` structures in the contigStore must be empty, i.e. there are no gaps in the contig. The pairwise alignment gaps of the reads are stored in the `gaps` structure in the alignedReadStore, whereas the pairwise alignment gaps of the contig are stored in the `pairwiseContigGaps` string.

After calling this functions all positions in the alignedReadStore are in gap-space.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void getClrRange(store, alignEl, begClr, endClr);`

Get the "clear" range of a read alignment.

#### Parameters

`store` | The FragmentStore to work on.
`alignEl` | The AlignedReadStoreElement to work on.
`begClr` | Begin of the clear range.
`endClr` | End of the clear range.

The clear range of a read alignment is the range of the part of the alignmetn that is not clipped.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `int getMateNo(store, readId);`

Returns the mate number for a read given a readId.

#### Parameters

`store` | The FragmentStore with the read.
`readId` | The readId.

#### Returns

`int` | The mate number (0 for the first mate, 1 for the second mate) of the read in its mate pair or -1 if the read is not paired.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TRead getRead(store, id);`

Returns the read with the given readId.

#### Parameters

`store` | The FragmentStore to query for the read.
`id` | The id of the read.

#### Returns

`TRead` | The entry from the readStore. TRead is the value type of the readStore.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool loadContig(store, contigId);`

Manually load a contig sequence.

#### Parameters

`store` | The FragmentStore to load the contig for.
`contigId` | The id of the contig that was created earlier by loadContigs.

#### Returns

`bool` | true on success, false on failure.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool loadContigs(store, fileName[, loadSeqs]); bool loadContigs(store, fileNameList[, loadSeqs]);`

Load contigs into a FragmentStore.

#### Parameters

`store` | The FragmentStore to append the contigs to.
`fileName` | A CharString with the name of the file to load.
`fileNameList` | A StringSet of CharString with a list of file names to load.
`loadSeqs` | A `bool` indicating whether to load lazily. If `true` then sequences are loaded immediately. If `false`, an emptycontig with a reference to the file is created. Its sequence can be loaded on demand by lockContig and loadContig.

#### Returns

`bool` | true in case of success and false in case of error.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool loadReads(store, fileName); bool loadReads(store, fileNameL, fileNameR);`

Loads reads into FragmentStore

#### Parameters

`store` | The FragmentStore to append the reads to.
`fileName` | Path to single-end read file.
`fileNameL` | Path to left read file in case of paired reads.
`fileNameR` | Path to right read file in case of paired reads.

#### Returns

`bool` | true in case of success, false in case of errors.

When two file names are given thent he files are expected to containt he same number of reads and reads with the same index are assumed to be mate pairs. Mate pairs are stored internally in an "interleaved mode": a read is read from each file before reading the next one.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool lockContig(store, contigId);`

Locks a contig sequence from being removed.

#### Parameters

`store` | The FragmentStore to lock the contig for.
`contigId` | The id of the contig that was created earlier by loadContigs.

#### Returns

`bool` | true on success, false on failure.

This function increases the contig usage counter by 1 and ensures that the contig sequence is loaded.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool lockContigs(store);`

Locks all contig sequences from being remove.

#### Parameters

`store` | The FragmentStore to lock the contigs for.

#### Returns

`bool` | true in case of success, false in case of errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `int read(file, store, tag);`

Read the contents of a FragmentStore from a file.

#### Parameters

`file` | The StreamConcept to read from.
`store` | The FragmentStore to append to.
`tag` | The format to read from. Can be Amos or Sam.

#### Returns

`int` | 0 in the case of success, non-0 value in case of errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void readRecords(store, bamFileIn[, importFlags]); void readRecords(store, gffFileIn); void readRecords(store, ucscFileIn);`

Read all records from a file.

#### Parameters

`store` | The FragmentStore object to store the records into.
`bamFileIn` | The BamFileIn object to read from.
`gffFileIn` | The GffFileIn object to read from.
`ucscFileIn` | The UcscFileIn object to read from.
`importFlags` | The import flags.

#### Thrown Exceptions

`IOError` | On low-level I/O errors.
`ParseError` | On high-level file format errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool unlockContig(store, contigId);`

Removes a previous contig lock and clears the sequence if no further lock exists.

#### Parameters

`store` | The FragmentStore to unlock the contig for.
`contigId` | The id of the contig that was created earlier by loadContigs.

#### Returns

`bool` | true on success, false on failure.

This function decreases the contig usage counter by 1 and frees the sequences' memory if the counter equals 0.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool unlockAndFreeContigs(store);`

Unlocks all contig sequences and clears sequences without lock.

#### Parameters

`store` | The FragmentStore to unlock the contigs for.

#### Returns

`bool` | true in case of success, false in case of errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool unlockContig(store, contigId);`

Removes a previous contig lock.

#### Parameters

`store` | The FragmentStore to unlock the contig for.
`contigId` | The id of the contig that was created earlier by loadContigs.

#### Returns

`bool` | true on success, false on failure.

This function decreases the contig usage counter by 1.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool unlockContigs(store);`

Unlocks all contig sequences.

#### Parameters

`store` | The FragmentStore to unlock the contigs for.

#### Returns

`bool` | true in case of success, false in case of errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `int write(file, store, tag);`

Write the contents of a FragmentStore to a file.

#### Parameters

`file` | The StreamConcept to write to.
`store` | The FragmentStore to write to the file.
`tag` | The format to write out. Types: Sam or Amos.

#### Returns

`int` | 0 in case of success, 1 in case of errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `bool writeContigs(file, store, tag);`

Write contigs from FragmentStore into a StreamConcept.

#### Parameters

`file` | The StreamConcept to write to.
`store` | The FragmentStore to write contigs of.
`tag` | A tag for the sequence format.

#### Returns

`bool` | true on success, false on errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void writeRecords(bamFileOut, store); void writeRecords(gffFileOut, store); void writeRecords(ucscFileIn, store);`

Write all records to a file.

#### Parameters

`bamFileOut` | The BamFileOut object to write into.
`gffFileOut` | The GffFileOut object to write into.
`ucscFileOut` | The UcscFileOut object to write into.
`store` | The FragmentStore object.

#### Thrown Exceptions

`IOError` | On low-level I/O errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Member Typedef Detail

### `typedef (..) TFragmentStore::TAlignedReadStore;`

Type of the alignedReadStore member.

### `typedef (..) TFragmentStore::TAlignedReadTagStore;`

Type of the alignedReadTagStore member.

### `typedef (..) TFragmentStore::TAlignQualityStore;`

Type of the alignQualityStore member.

### `typedef (..) TFragmentStore::TAnnotationKeyStore;`

Type of the annotationKeyStore member.

### `typedef (..) TFragmentStore::TAnnotationNameStore;`

Type of the annotationNameStore member.

### `typedef (..) TFragmentStore::TAnnotationStore;`

Type of the annotationStore member.

### `typedef (..) TFragmentStore::TAnnotationTypeStore;`

Type of the annotationTypeStore member.

### `typedef (..) TFragmentStore::TContigFileStore;`

Type of the contigFileStore member.

### `typedef (..) TFragmentStore::TContigNameStore;`

Type of the contigNameStore member.

### `typedef (..) TFragmentStore::TContigStore;`

Type of the contigStore member.

### `typedef (..) TFragmentStore::TLibraryNameStore;`

Type of the libraryNameStore member.

### `typedef (..) TFragmentStore::TMatePairNameStore;`

Type of the matePairNameStore member.

### `typedef (..) TFragmentStore::TMatePairStore;`

Type of the matePairStore member.

### `typedef (..) TFragmentStore::TReadNameStore;`

Type of the readNameStore member.

### `typedef (..) TFragmentStore::TReadSeqStore;`

Type of the readSeqStore member.

### `typedef (..) TFragmentStore::TReadStore;`

Type of the readStore member.

## Member Variables Detail

### `FragmentStore::TAlignedReadStore FragmentStore::alignedReadStore`

String that stores (alignId, readId, contigId, pairMatchId, beginPos, endPos, gapAnchors).

The value type is AlignedReadStoreElement.

#### Remarks

You can sort `alignedReadStore` using sortAlignedReads. After sorting, you can use the functions lowerBoundAlignedReads and upperBoundAlignedReads to perform a binary search, e.g. for accessing only a subrange.

### `FragmentStore::TAlignedReadTagStore FragmentStore::alignedReadTagStore`

StringSet that maps from alignId to alignTag.

### `FragmentStore::TAlignQualityStore FragmentStore::alignQualityStore`

String that maps from alignId to (pairScore, score, errors).

The value type is AlignQualityStoreElement.

### `FragmentStore::TAnnotationKeyStore FragmentStore::annotationKeyStore`

StringSet that maps from keyId to the name of a key. The keyId is used to address values of an annotation.

### `FragmentStore::TAnnotationNameStore FragmentStore::annotationNameStore`

StringSet that maps from annoId to annoName;

### `FragmentStore::TAnnotationStore FragmentStore::annotationStore`

String that maps from annoId to (contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values).

The value type is AnnotationStoreElement.

Instead of accessing this store directly, consider to use the high-level interface provided by AnnotationTreeIterator.

### `FragmentStore::TAnnotationTypeStore FragmentStore::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.

#### Remarks

There are predefined type ids for commonly used types e.g. `ANNO_GENE` or `ANNO_EXON` which can be used to set the typeId directly as a fast alternative to getType and setType.

### `FragmentStore::TContigFileStore FragmentStore::contigFileStore`

String that maps from contigId to (contigSeq, contigGaps, contigFileId).

Value type is ContigFile.

### `FragmentStore::TContigNameStore FragmentStore::contigNameStore`

StringSet that maps from contigId to contigName.

### `FragmentStore::TContigStore FragmentStore::contigStore`

String that maps from contigId to (contigSeq, contigGaps, contigFileId).

Value type is ContigStoreElement.

### `FragmentStore::TLibraryNameStore FragmentStore::libraryNameStore`

A StringSet that maps from libId to libName.

### `FragmentStore::TLibraryStore FragmentStore::libraryStore`

String that maps from libId to (mean, std).

Value type is LibraryStoreElement.

### `FragmentStore::TContigNameStore FragmentStore::matePairNameStore`

StringSet that maps from contigId to matePairName.

### `FragmentStore::TMatePairStore FragmentStore::matePairStore`

String that maps from matePairId to (readId[2], libId).

The value type is MatePairStoreElement.

### `FragmentStore::TReadNameStore FragmentStore::readNameStore`

StringSet that maps from readId to readName.

### `FragmentStore::TReadSeqStore FragmentStore::readSeqStore`

StringSet that maps from readId to readSeq.

### `FragmentStore::TReadStore FragmentStore::readStore`

A String that maps from readId to matePairId.

The value type is ReadStoreElement.

#### Dox Sources

    /*!
     * @class FragmentStore
     *
     * @headerfile <seqan/store.h>
     *
     * @brief Multi-container to store contigs, reads, multiple read alignments and
     *        genome annotations.
     *
     * @signature template <[typename TSpec[, typename TConfig]]> class
     *            FragmentStore;
     *
     * @tparam TSpec The specialializing type. Default: <tt>void</tt>.
     * @tparam TConfig The configuration struct. Default:
     *                 <tt>FragmentStoreConfig&lt;TSpec&gt;</tt>.
     *
     * 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.
     *
     * @section Examples
     *
     * Load read alignments and a reference genome and display the multiple
     * alignment in a genomic range:
     *
     * @include demos/dox/store/store_example.cpp
     *
     * @code{.console}
     * 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
     * @endcode
     *
     *
     * @section Remarks
     *
     * The following figures visualize the relations between the different stores:
     *
     * <img width="597" height="363" src="FragmentStore.png" title="Stores that are
     * involved in the representation of a multiple read alignment." />
     *
     * <img width="597" height="363" src="AnnotationStore.png" title="Stores that
     * are involved in the representation of a genome alignment." />
     *
     * @fn FragmentStore::clearReads
     *
     * @brief Removes all reds from a FragmentStore.
     *
     * @signature void clearReads(store);
     *
     * @param[in,out] store The FragmentStore to remove all reads from.
     *
     * Clears the @link FragmentStore::readStore @endlink, @link
     * FragmentStore::readSeqStore @endlink, and @link FragmentStore::readNameStore
     * @endlink.
     *
     * @typedef FragmentStore::TReadStore
     *
     * @brief Type of the @link FragmentStore::readStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TReadStore;
     *
     * @typedef FragmentStore::TReadSeqStore
     *
     * @brief Type of the @link FragmentStore::readSeqStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TReadSeqStore;
     *
     * @typedef FragmentStore::TMatePairStore
     *
     * @brief Type of the @link FragmentStore::matePairStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TMatePairStore;
     *
     * @typedef FragmentStore::TContigFileStore
     *
     * @brief Type of the @link FragmentStore::contigFileStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TContigFileStore;
     *
     * @typedef FragmentStore::TContigStore
     *
     * @brief Type of the @link FragmentStore::contigStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TContigStore;
     *
     * @typedef FragmentStore::TAlignedReadStore
     *
     * @brief Type of the @link FragmentStore::alignedReadStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAlignedReadStore;
     *
     * @typedef FragmentStore::TAnnotationStore
     *
     * @brief Type of the @link FragmentStore::annotationStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAnnotationStore;
     *
     * @typedef FragmentStore::TAlignQualityStore
     *
     * @brief Type of the @link FragmentStore::alignQualityStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAlignQualityStore;
     *
     * @typedef FragmentStore::TAlignedReadTagStore
     *
     * @brief Type of the @link FragmentStore::alignedReadTagStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAlignedReadTagStore;
     *
     * @typedef FragmentStore::TReadNameStore
     *
     * @brief Type of the @link FragmentStore::readNameStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TReadNameStore;
     *
     * @typedef FragmentStore::TMatePairNameStore
     *
     * @brief Type of the @link FragmentStore::matePairNameStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TMatePairNameStore;
     *
     * @typedef FragmentStore::TLibraryNameStore
     *
     * @brief Type of the @link FragmentStore::libraryNameStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TLibraryNameStore;
     *
     * @typedef FragmentStore::TContigNameStore
     *
     * @brief Type of the @link FragmentStore::contigNameStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TContigNameStore;
     *
     * @typedef FragmentStore::TAnnotationNameStore
     *
     * @brief Type of the @link FragmentStore::annotationNameStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAnnotationNameStore;
     *
     * @typedef FragmentStore::TAnnotationTypeStore
     *
     * @brief Type of the @link FragmentStore::annotationTypeStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAnnotationTypeStore;
     *
     * @typedef FragmentStore::TAnnotationKeyStore
     *
     * @brief Type of the @link FragmentStore::annotationKeyStore @endlink member.
     *
     * @signature typedef (..) TFragmentStore::TAnnotationKeyStore;
     *
     * @var FragmentStore::TReadStore FragmentStore::readStore;
     *
     * @brief A @link String @endlink that maps from readId to matePairId.
     *
     * The value type is @link ReadStoreElement @endlink.
     *
     * @var FragmentStore::TReadSeqStore FragmentStore::readSeqStore;
     *
     * @brief @link StringSet @endlink that maps from readId to readSeq.
     *
     * @var FragmentStore::TMatePairStore FragmentStore::matePairStore;
     *
     * @brief @link String @endlink that maps from matePairId to (readId[2], libId).
     *
     * The value type is @link MatePairStoreElement @endlink.
     *
     * @var FragmentStore::TLibraryStore FragmentStore::libraryStore;
     *
     * @brief @link String @endlink that maps from libId to (mean, std).
     *
     * Value type is @link LibraryStoreElement @endlink.
     *
     * @var FragmentStore::TContigFileStore FragmentStore::contigFileStore;
     *
     * @brief @link String @endlink that maps from contigId to (contigSeq,
     *        contigGaps, contigFileId).
     *
     * Value type is @link ContigFile @endlink.
     *
     * @var FragmentStore::TContigStore FragmentStore::contigStore;
     *
     * @brief @link String @endlink that maps from contigId to (contigSeq,
     *        contigGaps, contigFileId).
     *
     * Value type is @link ContigStoreElement @endlink.
     *
     * @var FragmentStore::TAlignedReadStore FragmentStore::alignedReadStore;
     *
     * @brief @link String @endlink that stores (alignId, readId, contigId,
     *        pairMatchId, beginPos, endPos, gapAnchors).
     *
     * The value type is @link AlignedReadStoreElement @endlink.
     *
     * @section Remarks
     *
     * You can sort <tt>alignedReadStore</tt> using @link sortAlignedReads @endlink.
     * After sorting, you can use the functions @link lowerBoundAlignedReads
     * @endlink and @link upperBoundAlignedReads @endlink to perform a binary
     * search, e.g. for accessing only a subrange.
     *
     * @see lowerBoundAlignedReads
     * @see upperBoundAlignedReads
     * @see sortAlignedReads
     *
     * @var FragmentStore::TAnnotationStore FragmentStore::annotationStore;
     *
     * @brief String that maps from annoId to (contigId, typeId, beginPos, endPos,
     *        parentId, lastChildId, nextSiblingId, values).
     *
     * The value type is @link AnnotationStoreElement @endlink.
     *
     * Instead of accessing this store directly, consider to use the high-level
     * interface provided by @link AnnotationTreeIterator @endlink.
     *
     * @var FragmentStore::TAlignQualityStore FragmentStore::alignQualityStore;
     *
     * @brief @link String @endlink that maps from alignId to (pairScore, score,
     *        errors).
     *
     * The value type is @link AlignQualityStoreElement @endlink.
     *
     * @var FragmentStore::TAlignedReadTagStore FragmentStore::alignedReadTagStore;
     *
     * @brief @link StringSet @endlink that maps from alignId to alignTag.
     *
     * @var FragmentStore::TReadNameStore FragmentStore::readNameStore;
     *
     * @brief @link StringSet @endlink that maps from readId to readName.
     *
     * @var FragmentStore::TContigNameStore FragmentStore::matePairNameStore;
     *
     * @brief @link StringSet @endlink that maps from contigId to matePairName.
     *
     * @var FragmentStore::TLibraryNameStore FragmentStore::libraryNameStore;
     *
     * @brief A @link StringSet @endlink that maps from libId to libName.
     *
     * @var FragmentStore::TContigNameStore FragmentStore::contigNameStore;
     *
     * @brief @link StringSet @endlink that maps from contigId to contigName.
     *
     * @var FragmentStore::TAnnotationNameStore FragmentStore::annotationNameStore;
     *
     * @brief @link StringSet @endlink that maps from annoId to annoName;
     *
     * @var FragmentStore::TAnnotationTypeStore FragmentStore::annotationTypeStore;
     *
     * @brief @link StringSet @endlink that maps from typeId to the type name of an
     *        annotation, e.g. "gene" or "exon". typeId is a member of the @link
     *        AnnotationStoreElement @endlink.
     *
     * @section Remarks
     *
     * There are @link FragmentStore::PredefinedAnnotationTypes predefined type ids
     * @endlink for commonly used types e.g. <tt>ANNO_GENE</tt> or
     * <tt>ANNO_EXON</tt> which can be used to set the @link
     * AnnotationStoreElement::typeId @endlink directly as a fast alternative to
     * @link AnnotationTreeIterator#getType @endlink and @link
     * AnnotationTreeIterator#setType @endlink.
     *
     * @var FragmentStore::TAnnotationKeyStore FragmentStore::annotationKeyStore;
     *
     * @brief @link StringSet @endlink that maps from keyId to the name of a key.
     *        The keyId is used to address @link AnnotationStoreElement::values
     *        @endlink of an annotation.
     *
     * @fn FragmentStore#getClrRange
     *
     * @brief Get the "clear" range of a read alignment.
     *
     * @signature void getClrRange(store, alignEl, begClr, endClr);
     *
     * @param[in] store The FragmentStore to work on.
     * @param[in] alignEl The @link AlignedReadStoreElement @endlink to work on.
     * @param[out] begClr Begin of the clear range.
     * @param[out] endClr End of the clear range.
     *
     * The clear range of a read alignment is the range of the part of the alignmetn
     * that is not clipped.
     *
     * @fn FragmentStore#read
     *
     * @brief Read the contents of a FragmentStore from a file.
     *
     * @signature int read(file, store, tag);
     *
     * @param[in,out] file The @link StreamConcept @endlink to read from.
     * @param[in,out] store The FragmentStore to append to.
     * @param[in] tag The format to read from. Can be Amos or Sam.
     *
     * @return int 0 in the case of success, non-0 value in case of errors.
     *
     * @fn FragmentStore#write
     *
     * @brief Write the contents of a FragmentStore to a file.
     *
     * @signature int write(file, store, tag);
     *
     * @param[in,out] file The @link StreamConcept @endlink to write to.
     * @param[in] store The FragmentStore to write to the file.
     * @param[in] tag The format to write out. Types: Sam or Amos.
     *
     * @return int 0 in case of success, 1 in case of errors.
     *
     * @fn FragmentStore#writeRecords
     *
     * @brief Write all records to a file.
     *
     * @signature void writeRecords(bamFileOut, store);
     * @signature void writeRecords(gffFileOut, store);
     * @signature void writeRecords(ucscFileIn, store);
     *
     * @param[in,out] bamFileOut The @link BamFileOut @endlink object to write into.
     * @param[in,out] gffFileOut The @link GffFileOut @endlink object to write into.
     * @param[in,out] ucscFileOut The @link UcscFileOut @endlink object to write
     *                            into.
     * @param[in] store The @link FragmentStore @endlink object.
     *
     * @throw IOError On low-level I/O errors.
     *
     * @fn FragmentStore#writeContigs
     *
     * @brief Write contigs from FragmentStore into a @link StreamConcept @endlink.
     *
     * @signature bool writeContigs(file, store, tag);
     *
     * @param[in,out] file The @link StreamConcept @endlink to write to.
     * @param[in] store The FragmentStore to write contigs of.
     * @param[in] tag A tag for the sequence format.
     *
     * @return bool true on success, false on errors.
     *
     * @fn FragmentStore#readRecords
     *
     * @brief Read all records from a file.
     *
     * @signature void readRecords(store, bamFileIn[, importFlags]);
     * @signature void readRecords(store, gffFileIn);
     * @signature void readRecords(store, ucscFileIn);
     *
     * @param[in,out] store The @link FragmentStore @endlink object to store the
     *                      records into.
     * @param[in,out] bamFileIn The @link BamFileIn @endlink object to read from.
     * @param[in,out] gffFileIn The @link GffFileIn @endlink object to read from.
     * @param[in,out] ucscFileIn The @link UcscFileIn @endlink object to read from.
     * @param[in] importFlags The import flags.
     *
     * @throw IOError On low-level I/O errors.
     * @throw ParseError On high-level file format errors.
     *
     * @fn FragmentStore#loadContigs
     *
     * @brief Load contigs into a FragmentStore.
     *
     * @signature bool loadContigs(store, fileName[, loadSeqs]);
     * @signature bool loadContigs(store, fileNameList[, loadSeqs]);
     *
     * @param[in,out] store The FragmentStore to append the contigs to.
     * @param[in] fileName A @link CharString @endlink with the name of the file to
     *                     load.
     * @param[in] fileNameList A @link StringSet @endlink of @link CharString
     *                         @endlink with a list of file names to load.
     * @param[in] loadSeqs A <tt>bool</tt> indicating whether to load lazily. If
     *                     <tt>true</tt> then sequences are loaded immediately. If
     *                     <tt>false</tt>, an emptycontig with a reference to the
     *                     file is created. Its sequence can be loaded on demand by
     *                     @link FragmentStore#lockContig @endlink and @link
     *                     FragmentStore#loadContig @endlink.
     *
     * @return bool true in case of success and false in case of error.
     *
     * @fn FragmentStore#loadContig
     *
     * @brief Manually load a contig sequence.
     *
     * @signature bool loadContig(store, contigId);
     *
     * @param[in,out] store The FragmentStore to load the contig for.
     * @param[in] contigId The id of the contig that was created earlier by @link
     *                     FragmentStore#loadContigs @endlink.
     *
     * @return bool true on success, false on failure.
     *
     * @fn FragmentStore#lockContig
     *
     * @brief Locks a contig sequence from being removed.
     *
     * @signature bool lockContig(store, contigId);
     *
     * @param[in,out] store The FragmentStore to lock the contig for.
     * @param[in] contigId The id of the contig that was created earlier by @link
     *                     FragmentStore#loadContigs @endlink.
     *
     * @return bool true on success, false on failure.
     *
     * This function increases the contig usage counter by 1 and ensures that the
     * contig sequence is loaded.
     *
     * @fn FragmentStore#unlockContig
     *
     * @brief Removes a previous contig lock.
     *
     * @signature bool unlockContig(store, contigId);
     *
     * @param[in,out] store The FragmentStore to unlock the contig for.
     * @param[in] contigId The id of the contig that was created earlier by @link
     *                     FragmentStore#loadContigs @endlink.
     *
     * @return bool true on success, false on failure.
     *
     * This function decreases the contig usage counter by 1.
     *
     * @fn FragmentStore#unlockAndFreeContig
     *
     * @brief Removes a previous contig lock and clears the sequence if no further
     *        lock exists.
     *
     * @signature bool unlockContig(store, contigId);
     *
     * @param[in,out] store The FragmentStore to unlock the contig for.
     * @param[in] contigId The id of the contig that was created earlier by @link
     *                     FragmentStore#loadContigs @endlink.
     *
     * @return bool true on success, false on failure.
     *
     * This function decreases the contig usage counter by 1 and frees the
     * sequences' memory if the counter equals 0.
     *
     * @fn FragmentStore#lockContigs
     *
     * @brief Locks all contig sequences from being remove.
     *
     * @signature bool lockContigs(store);
     *
     * @param[in,out] store The FragmentStore to lock the contigs for.
     *
     * @return bool true in case of success, false in case of errors.
     *
     * @fn FragmentStore#unlockContigs
     *
     * @brief Unlocks all contig sequences.
     *
     * @signature bool unlockContigs(store);
     *
     * @param[in,out] store The FragmentStore to unlock the contigs for.
     *
     * @return bool true in case of success, false in case of errors.
     *
     * @fn FragmentStore#unlockAndFreeContigs
     *
     * @brief Unlocks all contig sequences and clears sequences without lock.
     *
     * @signature bool unlockAndFreeContigs(store);
     *
     * @param[in,out] store The FragmentStore to unlock the contigs for.
     *
     * @return bool true in case of success, false in case of errors.
     *
     * @fn FragmentStore#loadReads
     *
     * @brief Loads reads into FragmentStore
     *
     * @signature bool loadReads(store, fileName);
     * @signature bool loadReads(store, fileNameL, fileNameR);
     *
     * @param[in,out] store The FragmentStore to append the reads to.
     * @param[in] fileName Path to single-end read file.
     * @param[in] fileNameL Path to left read file in case of paired reads.
     * @param[in] fileNameR Path to right read file in case of paired reads.
     *
     * @return bool true in case of success, false in case of errors.
     *
     * When two file names are given thent he files are expected to containt he same
     * number of reads and reads with the same index are assumed to be mate pairs.
     * Mate pairs are stored internally in an "interleaved mode": a read is read
     * from each file before reading the next one.
     *
     * @fn FragmentStore#clearContigs
     *
     * @brief REvmoes all contigs from a FragmentStore.
     *
     * @signature void clearContigs(store);
     *
     * @param[in,out] store The FragmentStore to remove all contigs from.
     *
     * This function clears the @link FragmentStore::contigStore @endlink and @link
     * FragmentStore::contigNameStore @endlink.
     *
     * @fn FragmentStore#appendRead
     *
     * @brief Append a read to a FragmentStore.
     *
     * @signature TSize appendRead(store, read[, matePairId]);
     * @signature TSize appendRead(store, read, name[, matePairId]);
     *
     * @param[in,out] store The FragmentStore to append the read to.
     * @param[in] read The read sequence. Type: @link ContainerConcept @endlink.
     * @param[in] name The name of the read. Type: @link CharString @endlink.
     * @param[in] matePairId ID of the mate-pair that this read is part of. Default:
     *                       <tt>FragmentStore::INVALID_ID</tt> which corresponds to
     *                       an unmated read.
     *
     * @return TSize The readId of the newly appended read. TSize is the size type
     *               of the @link FragmentStore::readStore @endlink.
     *
     * This funciton appends a single read to the @link FragmentStore::readStore
     * @endlink and @link FragmentStore::readSeqStore @endlink.
     *
     * @see FragmentStore#getRead
     *
     * @fn FragmentStore#getRead
     *
     * @brief Returns the read with the given readId.
     *
     * @signature TRead getRead(store, id);
     *
     * @param[in] store The FragmentStore to query for the read.
     * @param[in] id The id of the read.
     *
     * @return TRead The entry from the @link FragmentStore::readStore @endlink.
     *               TRead is the value type of the @link FragmentStore::readStore
     *               @endlink.
     *
     * @fn FragmentStore#appendAlignedRead
     *
     * @brief Appends an aligned read entyr to a fragment store.
     *
     * @signature TSize appendAlignedRead(store, readId, contigId, beginPos,
     *            endPos[, pairMatchId]);
     *
     * @param[in,out] store The FragmentStore to append to.
     * @param[in] readId The id of the read to append an alignment for.
     * @param[in] contigId The id of the contig of the alignment.
     * @param[in] beginPos The begin position of the alignment.
     * @param[in] endPos The end position of the alignment.
     * @param[in] pairMatchId The id of the alignedRead pair. Default:
     *                        <tt>FragmentStore::INVALID_ID</tt> which corresponds
     *                        to an unmated read.
     *
     * @return TSize The alignedReadId of the alignment.
     *
     * @section Remarks
     *
     * This function appends a single read alignment to the @link
     * FragmentStore::alignedReadStore @endlink. Note that this really only adds a
     * match. To generate a global alignment out of all these matches, use @link
     * FragmentStore#convertMatchesToGlobalAlignment @endlink.
     *
     * @see FragmentStore#appendRead
     *
     * @fn FragmentStore#appendMatePair
     *
     * @brief Appends the two reads of a mate pair to a FragmentStore.
     *
     * @signature TSize appendMatePair(store, readSeq1, readSeq2[, name1, name2]);
     *
     * @param[in,out] store The FragmentStore to append the mate pair to.
     * @param[in] readSeq1 The read sequence of the first read.
     * @param[in] readSeq2 The read sequence of the second read.
     * @param[in] name1 The read name of the first read.
     * @param[in] name2 The read name of the first read.
     *
     * @return TSize The matePairId of the newly appended mate pair. TSize is the
     *               size type of the @link FragmentStore::matePairStore @endlink.
     *
     * @section Remarks
     *
     * This function appends two reads to the @link FragmentStore::readStore
     * @endlink and @link FragmentStore::readSeqStore @endlink and a mate pair entry
     * for both them to the @link FragmentStore::matePairStore @endlink. If names
     * are given, they are appended to @link FragmentStore::readNameStore @endlink.
     *
     * @fn FragmentStore#compactAlignedReads
     *
     * @brief Remove invalid aligned reads and rename the alignId's sequentially
     *        beginning with 0.
     *
     * @signature TSize compactAlignedReads(store);
     *
     * @param[in,out] store The FragmentStore to compact the aligned reads of.
     *
     * @return s TSize The new size of the @link FragmentStore::alignedReadStore
     *           @endlink. TSize is the size type of the @link
     *           FragmentStore::alignedReadStore @endlink.
     *
     * @section Remarks
     *
     * This function removes all entries from the @link
     * FragmentStore::alignedReadStore @endlink whose alignId is equal to
     * <tt>INVALID_ID</tt> as well as orphan entries in @link
     * FragmentStore::alignQualityStore @endlink. Afterwards, the alignIds are
     * renamed sequentially beginning with 0. This function can be used to remove
     * alignments which are flagged by previously setting their id to INVALID_ID.
     *
     * @fn FragmentStore#compactPairMatchIds
     *
     * @brief Renames pairMatchId sequentially beginning with 0.
     *
     * @signature TSize compactPairMatchIds(store);
     *
     * @param[in,out] store The FragmentStore to compact pair match ids of.
     *
     * @return TSize The number of pair matches. TSize is the size type of @link
     *               FragmentStore::alignedReadStore @endlink.
     *
     * @section Remarks
     *
     * This function renames the pairMatchId in the @link
     * FragmentStore::alignedReadStore @endlink sequentially beginning with 0. Two
     * read alignments can be identified to be pair match if they have the same
     * pairMatchId. Please note that paired reads not necessarily have to map as a
     * pair match, e.g. if they are on different ocntigs or have the same
     * orientation or a wrong insert size.
     *
     * @fn FragmentStore#calculateInsertSizes
     *
     * @brief Calcualtes a string wtih insert sizes for each pair match.
     *
     * @signature void calculateInsertSizes(insertSizes, store);
     *
     * @param[out] insertSizes A @link String @endlink of insert sizes. This string
     *                         is accordingly resized and can be addressed by the
     *                         pairMatchId.
     * @param[in] store The @link FragmentStore @endlink to compute the insert sizes
     *                  for.
     *
     * @section Remarks
     *
     * This function calls @link FragmentStore#compactPairMatchIds @endlink first
     * and calcualte the insert size for every pair match. The insert size of a pair
     * match is the outer distance between the two matches.
     *
     * @fn FragmentStore#getMateNo
     *
     * @brief Returns the mate number for a read given a readId.
     *
     * @signature int getMateNo(store, readId);
     *
     * @param[in] store The FragmentStore with the read.
     * @param[in] readId The readId.
     *
     * @return int The mate number (0 for the first mate, 1 for the second mate) of
     *             the read in its mate pair or -1 if the read is not paired.
     *
     * @fn FragmentStore#calculateMateIndices
     *
     * @brief Calculates a string that maps the readId of a read to the index of its
     *        mate in the alignedReadStore.
     *
     * @signature void calculateMateIndices(mateIndices, store);
     *
     * @param[out] mateIndices A @link String @endlink with the resulting mate
     *                         indices. This string is accordingly resized and can
     *                         be addressed by the readId.
     * @param[in] store The @link FragmentStore @endlink.
     *
     * Entries of reads without a mate contain <tt>INVALID_ID</tt>.
     *
     * @fn FragmentStore#convertMatchesToGlobalAlignment
     *
     * @brief Converts all matches to a multiple global alignment in gap-space.
     *
     * @signature void convertMatchesToGlobalAlignment(store, score, shrinkMatches);
     *
     * @param[in,out] store The fragment store. Types: FragmentStore
     * @param[in] score A score object used by @link globalAlignment @endlink in
     *                  this function.
     * @param[in] shrinkMatches States whether the matches should be shrinked.
     *                          Types: True, False
     *
     * @section Remarks
     *
     * Before calling this function all <tt>gaps</tt> structures in @link
     * FragmentStore::alignedReadStore @endlink and @link FragmentStore::contigStore
     * @endlink must be empty, i.e. there are no gaps in the alignments. This
     * function iterates over entries in the @link FragmentStore::alignedReadStore
     * @endlink and semi-global aligns each read to its contig segments given by
     * begin and end position. Gaps introduced by these pair-wise alignments are
     * then inserted to the affected contig and reads correspondingly.
     *
     * The invariant that positions in the @link FragmentStore::alignedReadStore
     * @endlink are in gap-space holds before (there were no gaps in alignments) and
     * after calling this functions.
     *
     * If the @link FragmentStore::alignQualityStore @endlink of the @link
     * FragmentStore @endlink is empty when
     * <tt>convertMatchesToGlobalAlignment()</tt> is called then the @link
     * FragmentStore::alignQualityStore @endlink is filled with the edit distance
     * scores.
     *
     * @fn FragmentStore#convertPairWiseToGlobalAlignment
     *
     * @brief Converts pairwise alignments to a multiple global alignment.
     *
     * @signature void convertPairWiseToGlobalAlignment(store, pairwiseContigGaps);
     *
     * @param[in,out] store The fragment store. Types: FragmentStore
     * @param[in,out] pairwiseContigGaps  A @link String @endlink of anchored contig
     *                                   gaps for every pairwise alignment.
     *
     * @section Remarks
     *
     * Before calling this function the <tt>gaps</tt> structures in the @link
     * FragmentStore::contigStore @endlink must be empty, i.e. there are no gaps in
     * the contig. The pairwise alignment gaps of the reads are stored in the
     * <tt>gaps</tt> structure in the @link FragmentStore::alignedReadStore
     * @endlink, whereas the pairwise alignment gaps of the contig are stored in the
     * <tt>pairwiseContigGaps</tt> string.
     *
     * After calling this functions all positions in the @link
     * FragmentStore::alignedReadStore @endlink are in gap-space.
     */