diff test-data/lastz_d_ctrl_file.txt @ 5:bd84ff27bc16 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_d_ctrl_file.txt	Mon Feb 26 15:37:53 2018 -0500
@@ -0,0 +1,23 @@
+# base the inference on alignments in the middle half by identity
+min_identity       = 25.0%    # 25th percentile
+max_identity       = 75.0%    # 75th percentile
+
+# scale scores so max substitution score will be 100, and only use
+# alignments scoring at least as well as 20 ideal matches
+inference_scale    = 100      # max substitution score
+hsp_threshold      = 20*inference_scale
+gapped_threshold   = hsp_threshold
+
+# allow substitution score inference to iterate at most 20 times;
+# don't perform gap penalty inference -- instead hardwire gap penalties
+# relative to max substitution
+max_sub_iterations = 20
+max_gap_iterations = 0
+gap_open_penalty   = 4*inference_scale
+gap_extend_penalty = 0.3*inference_scale
+
+# use all seedword positions (don't sample)
+step               = 1
+
+# adjust for entropy when qualifying HSPs
+entropy            = on