Method that uses a gapped local affine exonerate alignment

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm

+package XrefMapper::Methods::ExonerateGappedBest1;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+
+  return ('--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+
+}
+
+
+
+1;