From 87453701b7292073cb9f80e91fc8e804df2103ca Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 6 Oct 2016 12:37:57 -0300
Subject: [PATCH] Change some parameters in program calls

Former-commit-id: 3ed8760844007def1d8c5a9cf4eaee01d571fe0b
Former-commit-id: b15127c8f8a601b33e09daccc645cbb8a1f23a2e
---
 detectors/cds/bin/do_exonerate.csh | 2 +-
 detectors/cds/lib/filterbx.awk     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/detectors/cds/bin/do_exonerate.csh b/detectors/cds/bin/do_exonerate.csh
index 7a8ca9c..c57b7fb 100755
--- a/detectors/cds/bin/do_exonerate.csh
+++ b/detectors/cds/bin/do_exonerate.csh
@@ -167,7 +167,7 @@ exonerate \
     --refine region                   \
     --refineboundary 5000             \
     --singlepass FALSE                \
-    --dpmemory 128                    \
+    --dpmemory 1024                   \
     $DbFile $GenoFile > $base.exo.raw
 CheckAbort 20 "exonerate failure"
 
diff --git a/detectors/cds/lib/filterbx.awk b/detectors/cds/lib/filterbx.awk
index cd232c2..775ad30 100644
--- a/detectors/cds/lib/filterbx.awk
+++ b/detectors/cds/lib/filterbx.awk
@@ -7,6 +7,7 @@ BEGIN {
   if (IDMIN == "")  IDMIN  = 80
   if (NBMIN == "")  NBMIN  = 50
   if (NBMAX == "")  NBMAX  = 200
+  if (COMIN == "")  COMIN  = 0.8  
 }
 
 /^#/ { next }