Class
LocalMatchStore
Stores information about local matches.
LocalMatchStore<[TSpec[, TConfig]]>
Include Headers
seqan/parse_lm.h
Parameters
TSpec
Specialization tag.
TConfig
Configuration class.
Remarks
The LocalMatchStore provides information about matches. Similar to the FragmentStore, the information is split into multiple sub stores. Each sub store stores a part of the information.
The matchStore stores the information about a match. The sequenceNameStore stores the sequence names. These both sub stores are "core stores", they are filled with consistent information, i.e. for each sequence id in the matchStore, there has to be a valid entry in the sequenceNameStore.
The cigarStore optionally stores CIGAR strings for the matches. Its entries are referenced by matchStore[i].id.
Data Members
cigarStoreString storing the CIGAR strings.
matchStoreString storing the local matches.
sequenceNameStoreStringSet storing the sequence names.
Functions
appendLocalMatchAppend a new local match to a LocalMatchStore
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
Examples
Read Lastz matches from a RecordReader and then print them to stdout.
// Read local alignments from record reader.  Note that in real-world code,
// you should have error handling.
LocalMatchStore<> lmStore;
while (!atEnd(recordReader))
    readRecord(lmStore, recordReader, StellarGff());
 
// Print local alignment information to stdout.
std::cout << "# Reverse strandness is indicated by end < begin\n"
          << "#db\tdb_beg\tdb_end\tquery\tq_beg\tq_end\n";
for (unsigned i = 0; i < length(lmStore.matchStore); ++i)
    std::cout << lmStore.sequenceNameStore[lmStore.matchStore[i].queryId] << "\t"
              << lmStore.matchStore[i].queryBeginPos << "\t"
              << lmStore.matchStore[i].queryEndPos << "\t"
              << lmStore.sequenceNameStore[lmStore.matchStore[i].subjectId] << "\t"
              << lmStore.matchStore[i].subjectBeginPos << "\t"
              << lmStore.matchStore[i].subjectEndPos << "\n";
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

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