add scorign to header and paramters and such

1 files changed, 5 insertions, 3 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
index 637ff2c..6010c08 100755
--- a/SelectiveGenomeAmplification
+++ b/SelectiveGenomeAmplification
@@ -147,6 +147,8 @@ done
 # output_top_nb, How many scored sets would you like in the top_scored_sets output file (Default = 10000)?
 : ${output_top_nb=10000}
 
+# scoring_func: A custom scoring function. disable by default. See README.md
+
 export ignore_mers
 export min_mer_range
 export max_mer_range
@@ -231,7 +233,7 @@ if [[ ! -d "$output_directory/$current_run/filter" ]]; then
 fi
 
 echo "Outputting current run parameters"
-	for var in ignore_mers ignore_all_mers_from_files 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 
+	for var in scoring_func ignore_mers ignore_all_mers_from_files 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;
 
@@ -323,8 +325,8 @@ if [[ -n "$step_score" ]] || [[ -n "$all" ]]; then
 	# output our sorted scores
 	echo "sorting and outputting top $output_top_nb scores"
 	echo "top scores output file: $output_directory/$current_run/top-scores"
-	head -n 2 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores
-	tail -n +3 $output_directory/$current_run/all-scores | sort -r -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores
+	head -n 3 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores
+	tail -n +4 $output_directory/$current_run/all-scores | sort -r -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores
 fi