guanguangua · guanguangua · Oct 30, 2019 · Oct 30, 2019 · Oct 30, 2019 · Oct 31, 2019
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,7 @@
 
 # Log file
 *.log
+*.err
 
 # BlueJ files
 *.ctxt

diff --git a/config/g1/action_ambiguous_mult_1.cfg b/config/g1/action_ambiguous_mult_1.cfg
@@ -0,0 +1,2 @@
+c@cat
+act@cat
diff --git a/config/g1/action_ambiguous_mult_2.cfg b/config/g1/action_ambiguous_mult_2.cfg
@@ -0,0 +1,2 @@
+t@c
+act@c
diff --git a/config/g1/action_pattern_overlap_mult_1.cfg b/config/g1/action_pattern_overlap_mult_1.cfg
@@ -0,0 +1,2 @@
+c;a;t@tag
+t;a;g@cat
diff --git a/config/g1/action_pattern_overlap_mult_2.cfg b/config/g1/action_pattern_overlap_mult_2.cfg
@@ -0,0 +1,3 @@
+g;g;g;g;g@aaaaa
+a;a;a;a;a@ttttt
+t;t;t;t;t@ggggg
diff --git a/config/g1/g1_sample_config.cfg b/config/g1/g1_sample_config.cfg
@@ -1,3 +1,3 @@
 c@cat
 a;acgt;c;acgt;g@t1g3c
-acgt@9876543210
+acgt@9876543210
diff --git a/config/g1/mult_mixed_1.cfg b/config/g1/mult_mixed_1.cfg
@@ -0,0 +1,2 @@
+c@cat
+a;acgt;g@g1a
diff --git a/config/g1/mult_mixed_2.cfg b/config/g1/mult_mixed_2.cfg
@@ -0,0 +1,2 @@
+c;a;t@tag
+a;acgt;c;acgt;g@t1g3c
diff --git a/config/g1/mult_mixed_3.cfg b/config/g1/mult_mixed_3.cfg
@@ -0,0 +1,2 @@
+a;acgt;c;acgt;g@t1g3c
+a;acgt;acgt;acgt;t@t321a
diff --git a/config/g1/mult_pure_char_1.cfg b/config/g1/mult_pure_char_1.cfg
@@ -0,0 +1,2 @@
+a;c@cc
+t@g
diff --git a/config/g1/mult_pure_char_2.cfg b/config/g1/mult_pure_char_2.cfg
@@ -0,0 +1,2 @@
+a;c;g;t@aaaa
+c@cat
diff --git a/config/g1/mult_pure_char_3.cfg b/config/g1/mult_pure_char_3.cfg
@@ -0,0 +1,2 @@
+ac;acg;ag;g@gattaca
+g;g@tag
diff --git a/config/g1/mult_pure_char_4.cfg b/config/g1/mult_pure_char_4.cfg
@@ -0,0 +1,3 @@
+a;c;g@ccg
+t;g@gc
+g;t;a@tag
diff --git a/config/g1/mult_pure_char_5.cfg b/config/g1/mult_pure_char_5.cfg
@@ -0,0 +1,3 @@
+ac;acgt;acgt;g@gattaca
+g;g;g@tag
+c;a;t@ttt
diff --git a/config/g1/pattern_ambiguous_mult_1.cfg b/config/g1/pattern_ambiguous_mult_1.cfg
@@ -0,0 +1,2 @@
+c;a;t;c;a;t@aaaaaa
+c;a;t;c;a@ccccc
diff --git a/config/g1/pattern_ambiguous_mult_2.cfg b/config/g1/pattern_ambiguous_mult_2.cfg
@@ -0,0 +1,2 @@
+a;a;a@ttt
+a;a;a;a@gggg
diff --git a/config/g1/pattern_ambiguous_mult_3.cfg b/config/g1/pattern_ambiguous_mult_3.cfg
@@ -0,0 +1,2 @@
+a@c
+a@g
diff --git a/config/g1/single_mixed_1.cfg b/config/g1/single_mixed_1.cfg
@@ -0,0 +1 @@
+a;acgt;c;acgt;g@t3g1c
diff --git a/config/g1/single_mixed_2.cfg b/config/g1/single_mixed_2.cfg
@@ -0,0 +1 @@
+a;ac;gt@g12
diff --git a/config/g1/single_mixed_3.cfg b/config/g1/single_mixed_3.cfg
@@ -0,0 +1 @@
+a;acgt;acgt;acgt;t@t321a
diff --git a/config/g1/single_mixed_4.cfg b/config/g1/single_mixed_4.cfg
@@ -0,0 +1 @@
+a;acgt;t@g1gaa
diff --git a/config/g1/single_mixed_5.cfg b/config/g1/single_mixed_5.cfg
@@ -0,0 +1 @@
+a;acgt;cgt;gt@g123a
diff --git a/config/g1/single_pure_char_1.cfg b/config/g1/single_pure_char_1.cfg
@@ -0,0 +1 @@
+a;c@c
diff --git a/config/g1/single_pure_char_2.cfg b/config/g1/single_pure_char_2.cfg
@@ -0,0 +1 @@
+a;acg;g@cat
diff --git a/config/g1/single_pure_char_3.cfg b/config/g1/single_pure_char_3.cfg
@@ -0,0 +1 @@
+ac;acg;ag;g@gattaca
diff --git a/config/g1/single_pure_char_4.cfg b/config/g1/single_pure_char_4.cfg
@@ -0,0 +1 @@
+c;acgt;acgt;acgt;acgt;acgt;acgt;t@ttt
diff --git a/config/g1/single_pure_char_5.cfg b/config/g1/single_pure_char_5.cfg
@@ -0,0 +1 @@
+c;acgt;acgt;acgt;acgt;acgt;acgt;acgt;acgt;t@acgtacgtac
diff --git a/config/g1/single_pure_numeric_1.cfg b/config/g1/single_pure_numeric_1.cfg
@@ -0,0 +1 @@
+acg;acgt;acg@210
diff --git a/config/g1/single_pure_numeric_2.cfg b/config/g1/single_pure_numeric_2.cfg
@@ -0,0 +1 @@
+c@8
diff --git a/config/g1/single_pure_numeric_3.cfg b/config/g1/single_pure_numeric_3.cfg
@@ -0,0 +1 @@
+acgt@321
diff --git a/config/g1/single_pure_numeric_4.cfg b/config/g1/single_pure_numeric_4.cfg
@@ -0,0 +1 @@
+a;c@3344
diff --git a/config/g1/tournament.cfg b/config/g1/tournament.cfg
@@ -0,0 +1,2 @@
+c;a;t@tag
+g@3
diff --git a/config/g2/simple.cfg b/config/g2/simple.cfg
@@ -1 +1 @@
-agt;c;tgc@caa
+a;c;g;t@gattaca
diff --git a/config/g2/simple2.cfg b/config/g2/simple2.cfg
@@ -0,0 +1 @@
+a;c;g;t@ctaa
diff --git a/config/g2/simple3.cfg b/config/g2/simple3.cfg
@@ -0,0 +1,3 @@
+a;ca;g;tc@ct1a
+a;c;t;g@gattaca
+c;a;t@210
diff --git a/config/g2/simple4.cfg b/config/g2/simple4.cfg
@@ -0,0 +1 @@
+c;a;t@210
diff --git a/config/g2/simple5.cfg b/config/g2/simple5.cfg
@@ -0,0 +1,4 @@
+a;ca;g;tc@ct1a
+a;c;t;g@gattaca
+c;a;t@210
+a;c;g;t@ctaa
diff --git a/config/g2/tournament.cfg b/config/g2/tournament.cfg
@@ -0,0 +1,3 @@
+a;ca;g;tc@ct1a
+a;c;t;g@gattaca
+c;a;t@tac
diff --git a/config/g3/mutagen_bigswap.cfg b/config/g3/mutagen_bigswap.cfg
@@ -1 +1 @@
-acgt;acgt;act;acgt@2301
+acgt;acgt;act@2301
diff --git a/config/g3/mutagen_class.cfg b/config/g3/mutagen_class.cfg
@@ -0,0 +1 @@
+t;a;g@gattaca
diff --git a/config/g3/mutagen_class2.cfg b/config/g3/mutagen_class2.cfg
@@ -0,0 +1,2 @@
+a;c;c;g@gtca
+cg;a;t@210
diff --git a/config/g3/mutagen_s3.cfg b/config/g3/mutagen_s3.cfg
@@ -0,0 +1 @@
+a;c;ctg;ag;acg;acgt;acgt@gtca03a
diff --git a/config/g3/tournament.cfg b/config/g3/tournament.cfg
@@ -0,0 +1,2 @@
+c;ct;a;t@0a23g
+ac;t;actg;ag;ct@c12t4
diff --git a/config/g4/tournament.cfg b/config/g4/tournament.cfg
@@ -0,0 +1,2 @@
+c;a;g;t@atata
+ac;a;ac;a@0gg
diff --git a/config/g5/tournament.cfg b/config/g5/tournament.cfg
@@ -0,0 +1,2 @@
+a;g;c@cgt
+a@5
diff --git a/config/g6/mutagen.cfg b/config/g6/mutagen.cfg
@@ -1 +1,2 @@
-c;g;t;a@tact
+ct;ac;t@agt09
+ga;at;t@gattaca
diff --git a/config/g6/tournament.cfg b/config/g6/tournament.cfg
@@ -0,0 +1,2 @@
+ct;ac;t@agt0
+ga;at;t@gattaca
diff --git a/config/g7/test_cases/double.cfg b/config/g7/test_cases/double.cfg
@@ -0,0 +1,2 @@
+a;c;c;g@gtca
+cg;a;t@210
diff --git a/config/g7/test_cases/double_simple.cfg b/config/g7/test_cases/double_simple.cfg
@@ -0,0 +1,2 @@
+a@t
+a;g@ga
diff --git a/config/g7/test_cases/double_vague.cfg b/config/g7/test_cases/double_vague.cfg
@@ -0,0 +1,4 @@
+a;c;c;g@gtca
+a;t;a@taa
+a;t;c@tac
+a;t;g@tag
diff --git a/config/g7/test_cases/end_same.cfg b/config/g7/test_cases/end_same.cfg
@@ -0,0 +1 @@
+a;c;g;t@cgtt
diff --git a/config/g7/test_cases/inversion.cfg b/config/g7/test_cases/inversion.cfg
@@ -0,0 +1 @@
+acgt;a;c@011
diff --git a/config/g7/test_cases/last_dif.cfg b/config/g7/test_cases/last_dif.cfg
@@ -0,0 +1 @@
+a;c;g;t;acg@gtat
diff --git a/config/g7/test_cases/middle.cfg b/config/g7/test_cases/middle.cfg
@@ -0,0 +1 @@
+a;g;g;t@cgtt
diff --git a/config/g7/test_cases/permutation.cfg b/config/g7/test_cases/permutation.cfg
@@ -0,0 +1 @@
+acg;act;ta;a;ta@20143
diff --git a/config/g7/test_cases/short_action.cfg b/config/g7/test_cases/short_action.cfg
@@ -0,0 +1 @@
+g;c;a;t@c
diff --git a/config/g7/test_cases/short_pattern.cfg b/config/g7/test_cases/short_pattern.cfg
@@ -0,0 +1 @@
+a;c;g;acgt@catt
diff --git a/config/g7/test_cases/short_pattern_our_form.cfg b/config/g7/test_cases/short_pattern_our_form.cfg
@@ -0,0 +1,4 @@
+a;c;g;a@catt
+a;c;g;c@catt
+a;c;g;g@catt
+a;c;g;t@catt
diff --git a/config/g7/test_cases/single_vague.cfg b/config/g7/test_cases/single_vague.cfg
@@ -0,0 +1 @@
+a;acgt;t@t1a
diff --git a/config/g7/test_cases/single_vague_long.cfg b/config/g7/test_cases/single_vague_long.cfg
@@ -0,0 +1 @@
+a;cgt;t;acg;g@t3a1c
diff --git a/config/g7/test_cases/single_vague_long_2.cfg b/config/g7/test_cases/single_vague_long_2.cfg
@@ -0,0 +1 @@
+a;cgta;t;acgt;g@t3a1c
diff --git a/config/g7/test_cases/start_same.cfg b/config/g7/test_cases/start_same.cfg
@@ -0,0 +1 @@
+a;c;g;t@cgtt
diff --git a/config/g7/test_cases/triple_simple.cfg b/config/g7/test_cases/triple_simple.cfg
@@ -0,0 +1,3 @@
+a@t
+c;t@ga
+g;t;t@aaa
diff --git a/config/g7/test_cases/two_rule.cfg b/config/g7/test_cases/two_rule.cfg
@@ -0,0 +1,2 @@
+c;a;t;g@tatc
+t;a;g@gat
diff --git a/config/g7/test_cases/vague.cfg b/config/g7/test_cases/vague.cfg
@@ -0,0 +1,3 @@
+a;t;a@taa
+a;t;c@tac
+a;t;g@tag
diff --git a/config/g7/tournament.cfg b/config/g7/tournament.cfg
@@ -0,0 +1,2 @@
+c;a;t;g@tatc
+t;a;g@gat
diff --git a/config/g8/tournament.cfg b/config/g8/tournament.cfg
@@ -0,0 +1 @@
+c;acg;t@11g
diff --git a/config/tournament/simple.cfg b/config/tournament/simple.cfg
@@ -0,0 +1,2 @@
+a@t
+g@c
diff --git a/config/tournament/single.cfg b/config/tournament/single.cfg
@@ -0,0 +1 @@
+ac;gt;g@tcc
diff --git a/config/tournament/single2.cfg b/config/tournament/single2.cfg
@@ -0,0 +1 @@
+a;acgt;c;acgt;g@987atc
diff --git a/config/tournament/t1.cfg b/config/tournament/t1.cfg
@@ -0,0 +1,2 @@
+c;c@tt
+c@t
diff --git a/config/tournament/t2.cfg b/config/tournament/t2.cfg
@@ -0,0 +1,2 @@
+acg;cgt;agt;act@tacgg
+t;a;c;g;g@gtacg
diff --git a/config/tournament/t3.cfg b/config/tournament/t3.cfg
@@ -0,0 +1,3 @@
+t;c;a;t;g@atccg
+a;t;c;c;g@tcatg
+a;t;c@g98
diff --git a/config/tournament/t4.cfg b/config/tournament/t4.cfg
@@ -0,0 +1,3 @@
+t;c;a;t;g;c@atccgt
+a;t;c;c;g;t@tcatgc
+a;t;c@gat
diff --git a/mutagen.cfg b/mutagen.cfg
@@ -1,2 +1 @@
-g@ga
-g@gag
+ac@3355
diff --git a/mutation/g3/.DS_Store → mutation/.DS_Store b/mutation/g3/.DS_Store → mutation/.DS_Store