# HG changeset patch
# User mheinzl
# Date 1616062464 0
# Node ID fd342f5a97d97bd101f1afaaebcb8a1aa056d8b2
# Parent  f0fc93b7945cd2624fc0b1cca02f5f4544f3aced
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r f0fc93b7945c -r fd342f5a97d9 read2mut.py
--- a/read2mut.py	Thu Mar 18 10:07:50 2021 +0000
+++ b/read2mut.py	Thu Mar 18 10:14:24 2021 +0000
@@ -962,42 +962,42 @@
                             tier_dict[key1]["tier 4"] += 1
 
                         	# assign tiers
-                        	if ((all(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
-                        	     all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) |
-                        	    (all(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
-                        	     all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
-                        	    trimmed_actual_high_tier = True
-                        	elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) &
-                        	      any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
-                        	      any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
-                        	      all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])):
+                            if ((all(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
+                                 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) |
+                                (all(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
+                                 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
+                                trimmed_actual_high_tier = True
+                            elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) &
+                                  any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
+                                  any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
+                                  all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])):
                         	    trimmed_actual_high_tier = True
                         	elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) &
                         	       any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
                         	       all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) |
-                        	      (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
-                        	       any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
-                        	       all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
-                        	    trimmed_actual_high_tier = True
-                        	elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) &
-                        	      all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt2ff_trim, alt3ff_trim, alt4ff_trim])):
-                        	    trimmed_actual_high_tier = True
-                        	elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) &
-                        	       any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
-                        	       all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]) &
-                        	       any(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim])) |
-                        	      (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
-                        	       any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
-                        	       all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]) &
-                        	       any(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]))):
-                        	    trimmed_actual_high_tier = True
-                        	elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) &
-                        	       all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) |
-                        	      (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
-                        	       all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
-                        	    trimmed_actual_high_tier = True
-                        	else:
-                        		trimmed_actual_high_tier = False
+                                  (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
+                                   any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
+                                   all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
+                                trimmed_actual_high_tier = True
+                            elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) &
+                                  all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt2ff_trim, alt3ff_trim, alt4ff_trim])):
+                                trimmed_actual_high_tier = True
+                            elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) &
+                                   any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) &
+                                   all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]) &
+                                   any(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim])) |
+                                  (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
+                                   any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) &
+                                   all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]) &
+                                   any(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]))):
+                                trimmed_actual_high_tier = True
+                            elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) &
+                                   all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) |
+                                  (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) &
+                                   all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))):
+                                trimmed_actual_high_tier = True
+                            else:
+                                trimmed_actual_high_tier = False
 
                         elif softclipped_mutation_allMates:
                             tier = "5.1"