--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/funannotate_db/trained_species/fly/augustus/fly_metapars.cfg	Mon Oct 04 19:39:38 2021 +0000
@@ -0,0 +1,48 @@
+# This file contains the list of meta parameters for the coding regions (CDS) which are subject to optimization. 
+# All other meta parameters are chosen as given in the species parameter file. The order 
+# of the parameters determines the order in the optimization process.
+# Basically, different values for these meta parameters are tried out and the ones
+# giving best performance in a cross-validation on the training set are chosen.
+# For each parameter the range of possible values is specified after the parameter
+# name and at least one white space.
+# 3 cases are possible for the range:
+# - an explicit list is given, e.g. protein	"on" "off"
+# - it is an integer range, e.g. window_size	"1"-"5"
+# - it is a range of floating point numbers, e.g. pseudocount	"0.3"_"1.8"
+#
+# 
+# Mario Stanke, 19.12.2006
+#
+
+/Constant/dss_end		"1"-"4"
+/Constant/dss_start		"1"-"3"
+/Constant/ass_start		"1"-"3"
+/Constant/ass_end		"0"-"4"
+/Constant/ass_upwindow_size	"1"-"50"
+/IntronModel/d                  "100"-"950"
+/IntronModel/ass_motif_memory	"0"-"3"
+/IntronModel/ass_motif_radius	"0"-"4"
+/ExonModel/tis_motif_memory	"0"-"3"
+/ExonModel/tis_motif_radius	"0"-"3"
+/Constant/trans_init_window	"0"-"25"
+/Constant/init_coding_len	"0"-"18"
+/ExonModel/patpseudocount	"0.5"_"5"
+/ExonModel/etpseudocount	"0"-"10"
+/ExonModel/etorder		"0"-"3"
+/Constant/intterm_coding_len	"0"-"13"
+/ExonModel/slope_of_bandwidth	"0.05"_"0.6"
+/ExonModel/minwindowcount	"1"-"15"
+/IGenicModel/patpseudocount	"0.5"_"7"
+/IntronModel/patpseudocount	"0.5"_"7"
+/IntronModel/slope_of_bandwidth	"0.05"_"0.6"
+/IntronModel/minwindowcount	"1"-"8"
+/IntronModel/asspseudocount	"0.0005"_"0.03"
+/IntronModel/dsspseudocount	"0.0002"_"0.04"
+/IntronModel/dssneighborfactor  "0.0001"_"0.01"
+/ExonModel/minPatSum		"100"_"600"
+/Constant/probNinCoding         "0.15"_".25"
+/Constant/decomp_num_steps	"1"-"5"
+# comment parameters out that you do not want to be subject of optimization
+#/IGenicModel/k                  "4" "3" "5"
+#/IntronModel/k                  "4" "3" "5"
+#/ExonModel/k                    "4" "3" "5"