From 1990ed3dce20d2ff0cb0fafb5acf1410e74d96f1 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 13 Nov 2007 10:26:15 +0000
Subject: [PATCH] added -gappedextension FALSE to make it faster
---
.../xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm | 2 +-
.../XrefMapper/Methods/ExonerateGappedBest1_agam.pm | 2 +-
.../XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm
index 4ca1566b27..31e522d843 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm
@@ -10,7 +10,7 @@ use vars '@ISA';
sub options {
- return ('--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+ return ('-gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
index 9d11f74b44..8011434127 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
@@ -9,7 +9,7 @@ use vars '@ISA';
sub options {
- return ('--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+ return ('-gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
}
sub query_identity_threshold {
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm
index 5b762ff282..2b2e30ec8d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm
@@ -10,7 +10,7 @@ use vars '@ISA';
sub options {
- return ('--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+ return ('-gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
}
--
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