From e373466634459abcb67d8f189d9a67692d5a1ae2 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 12 Feb 2010 15:08:43 +0000
Subject: [PATCH] gapped alignment at 100 percent
---
.../ExonerateGappedBest_100_perc_id.pm | 30 +++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.pm
new file mode 100644
index 0000000000..a93fb65996
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.pm
@@ -0,0 +1,30 @@
+package XrefMapper::Methods::ExonerateGappedBest_100_perc_id;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+
+ return ('--gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+
+}
+
+sub query_identity_threshold {
+
+ return 100;
+
+}
+
+sub target_identity_threshold {
+
+ return 100;
+
+}
+
+
+1;
--
GitLab