From ea35050608ef170a17bcb8c3a4da431bb9e63f65 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Thu, 3 May 2012 16:04:31 +0000
Subject: [PATCH] replaced with ExonerateGappedBest1_55_perc_id
---
.../Methods/ExonerateGappedBest1_agam.pm | 25 ------------------
.../Methods/ExonerateGappedBest1_culex.pm | 26 -------------------
2 files changed, 51 deletions(-)
delete mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
delete mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
deleted file mode 100644
index 80ea69c2d5..0000000000
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm
+++ /dev/null
@@ -1,25 +0,0 @@
-package XrefMapper::Methods::ExonerateGappedBest1_agam;
-
-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 55;
-}
-
-sub target_identity_threshold {
- return 55;
-}
-
-
-1;
-
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
deleted file mode 100644
index 544371a697..0000000000
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
+++ /dev/null
@@ -1,26 +0,0 @@
-package XrefMapper::Methods::ExonerateGappedBest1_culex;
-
-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 55;
-}
-
-sub target_identity_threshold {
- return 55;
-}
-
-
-1;
--
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