Update AlignerMain.cpp

Author: alexandrutomescu

src/AlignerMain.cpp

@@ -105,6 +105,7 @@ int main(int argc, char** argv)
 ("greedy-length", "greedily select a non-overlapping alignment set based on alignment length")
 ("greedy-E", "greedily select a non-overlapping alignment set based on E-value")
 ("greedy-score", "greedily select a non-overlapping alignment set based on alignment score")
+("no-colinear-chaining", "do not run colinear chaining and align as in GraphAligner, default parameters")
 ;
 
 boost::program_options::options_description cmdline_options;
@@ -194,6 +195,9 @@ int main(int argc, char** argv)
 if (vm.count("fast-mode"))
 params.fastMode = true;
 
+if (vm.count("no-colinear-chaining"))
+params.colinearChaining = false;
+
 if (params.colinearChaining)
 {
 params.alignmentSelectionMethod = AlignmentSelection::SelectionMethod::All;