Class
LocalMatchStore
Stores information about local matches.
Include Headers
seqan/parse_lm.h
Parameters
Specialization tag. | |
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
String storing the CIGAR strings. | |
String storing the local matches. | |
StringSet storing the sequence names. |
Functions
Append a new local match to a LocalMatchStore | |
reads 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.
// 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