add primer_weight to our score function

1 files changed, 6 insertions, 2 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
index b875fe0..ad8d4a5 100755
--- a/SelectiveGenomeAmplification
+++ b/SelectiveGenomeAmplification
@@ -56,9 +56,12 @@ fi
 # maximum number of mers that are consecutively binding
 : ${max_consecutive_binding=4}
 
-# fg_weight, now much to weight to give the higher bindnig primers
+# fg_weight, how much to weight to give the higher bindnig primers
 : ${fg_weight=0}
 
+# primer_weight, how much weight to give to sets with a higher number of priemrs. (between 0 and 1)
+: ${primer_weight=0}
+
 export ignore_mers
 export min_mer_range
 export max_mer_range
@@ -72,6 +75,7 @@ export max_melting_temp
 export min_melting_temp 
 
 export fg_weight
+export primer_weight
 
 
 # Make our output directory
@@ -131,7 +135,7 @@ if [ "$ignore_mers" ]; then
 fi
 
 echo "outputing current run parameters"
-for var in ignore_mers min_mer_range max_check cpus max_consecutive_binding max_mer_range max_select min_mer_count max_mer_distance max_melting_temp min_melting_temp foreground background; do 
+for var in ignore_mers min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do 
  echo $var "${!var}" >> $output_directory/$current_run/parameters
 done;