ToC
In the next example we are going to use the Swift filter to efficiently find pairs of similar reads. The Swift algorithm searches for so-called epsilon matches (local alignments) of two sequences with an error rate below a certain epsilon threshold.
The Swift implementation in SeqAn provides a Finder#find interface and requires the Finder and Pattern to be specialized with Swift<..>. Millions of sequences can be searched simultaneously with one SwiftPattern Swift Pattern in a SwiftFinder Swift Finder of a single haystack sequence. The error rate of a local alignment is the number of errors divided by the length of the needle sequence part of the match. There are currently two version of the Swift algorithm implemented in SeqAn: SwiftSemiGlobal and SwiftLocal. Both can be used to search epsilon-matches of a certain minimum length.
Hint
SwiftSemiGlobal should only be used for short needles (sequenced reads) as it always returns potential epsilon matches spanning a whole needle sequence. SwiftLocal should be preferred for large needles as it returns needle sequences potentially having an intersection with an epsilon match.
The following program searches for semi-global alignments between pairs of reads with a maximal error rate of 10%.
demos/howto/filter_similar_sequences.cpp
First we loads reads from a file into a FragmentStore with FragmentStore#loadReads.
demos/howto/filter_similar_sequences.cpp
Swift uses a q-gram index of the needle sequences. Thus, we have to specialize the SwiftSemiGlobalPattern Swift Semi Global Pattern with a IndexQGram index of the needle StringSet in the first template argument, create the index over the FragmentStore::readSeqStore and pass the index to the SwiftSemiGlobalPattern Pattern constructor. SwiftSemiGlobalFinder Swift Semi Global Finder and SwiftSemiGlobalPattern Swift Semi Global Pattern classes have to be specialized with SwiftSemiGlobal in the second template argument.
Note
Note, to use the local swift filter you simply switch the specialization tag to SwiftLocal: SwiftLocalFinder Swift Local Finder and SwiftLocalPattern Swift Local Pattern.
The main loop iterates over all potential matches which can be further processed, e.g. by a semi-global or overlap aligner.
demos/howto/filter_similar_sequences.cpp