From 40d0c406ba7475546c03838c246898798e2c0482 Mon Sep 17 00:00:00 2001
From: mestato <mstaton1@utk.edu>
Date: Mon, 20 Jul 2015 21:55:51 -0400
Subject: [PATCH] Added primer3 parameter to utilize masking.

---
 hwg_gssr_scripts/findSSRs_fasta.pl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/hwg_gssr_scripts/findSSRs_fasta.pl b/hwg_gssr_scripts/findSSRs_fasta.pl
index 7a213b0..2cb0fa3 100755
--- a/hwg_gssr_scripts/findSSRs_fasta.pl
+++ b/hwg_gssr_scripts/findSSRs_fasta.pl
@@ -122,6 +122,8 @@
 my $PRIMER_MAX_POLY_X = "3";
 my $PRIMER_GC_CLAMP = "2";
 
+my $PRIMER_LOWERCASE_MASKING = 1;
+
 #-------------------------------------------------------------------------------
 # GLOBAL HASHES
 #-------------------------------------------------------------------------------
@@ -566,6 +568,7 @@ sub addToPrimer3InputFile{
     		printf OUT ("PRIMER_MAX_POLY_X=$PRIMER_MAX_POLY_X\n");
     		printf OUT ("PRIMER_GC_CLAMP=$PRIMER_GC_CLAMP\n");
     		printf OUT ("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=$PRIMER3_CONFIG\n");
+    		printf OUT ("PRIMER_LOWERCASE_MASKING=$PRIMER_LOWERCASE_MASKING\n");
     		printf OUT ("=\n");
 		}
 	}