output parameters

1 files changed, 4 insertions, 1 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
index 9358e39..d5e1780 100755
--- a/SelectiveGenomeAmplification
+++ b/SelectiveGenomeAmplification
@@ -102,7 +102,6 @@ for fasta_file in $foreground $background; do
 	done
 done
 
-
 fg_counts=$counts_directory/$(basename $foreground)-counts
 bg_counts=$counts_directory/$(basename $background)-counts
 
@@ -120,6 +119,10 @@ if [ "$ignore_mers" ]; then
 	done
 fi
 
+echo "outputing current run parameters"
+for var in ignore_mers min_mer_range max_mer_range max_select min_mer_count max_mer_distance max_melting_temp min_melting_temp; do
+ echo $var "${!var}" >> $output_directory/$current_run/parameters
+done;
 
 echo "checking if mers are below melting temperature in the foreground"
 rm $fg_counts-non-melting