# HG changeset patch
# User mheinzl
# Date 1603802361 0
# Node ID 386438cd4c3b448f686d3ef221fd5ecb3e074b28
# Parent  4fc62ab6e9e8516e97a0344c7f3df37bd010bc40
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 4fc62ab6e9e8 -r 386438cd4c3b read2mut.py
--- a/read2mut.py	Sat Oct 17 09:11:53 2020 +0000
+++ b/read2mut.py	Tue Oct 27 12:39:21 2020 +0000
@@ -231,7 +231,7 @@
                    'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba',
                    'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', 'trim.ab', 'trim.ba',
                    'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba',
-                   'other mut', 'chimeric tag')
+                   'in phase', 'chimeric tag')
     ws1.write_row(0, 0, header_line)
 
     counter_tier11 = 0
@@ -320,10 +320,11 @@
                             if add_mut1 > 1:
                                 for k, v in mut_read_dict[(key2[:-5] + '.ab.1')].items():
                                     if k != key1:
+                                        new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0]
                                         if len(add_mut14) == 0:
-                                            add_mut14 = str(k) + "_" + v
+                                            add_mut14 = new_mut
                                         else:
-                                            add_mut14 = add_mut14 + ", " + str(k) + "_" + v
+                                            add_mut14 = add_mut14 + ", " + new_mut
                         else:
                             k1 = []
                     else:
@@ -362,10 +363,11 @@
                             if add_mut2 > 1:
                                 for k, v in mut_read_dict[(key2[:-5] + '.ab.2')].items():
                                     if k != key1:
+                                        new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0]
                                         if len(add_mut23) == 0:
-                                            add_mut23 = str(k) + "_" + v
+                                            add_mut23 = new_mut
                                         else:
-                                            add_mut23 = add_mut23 + ", " + str(k) + "_" + v
+                                            add_mut23 = add_mut23 + ", " + new_mut
                         else:
                             k2 = []
                     else:
@@ -403,10 +405,11 @@
                             if add_mut3 > 1:
                                 for k, v in mut_read_dict[(key2[:-5] + '.ba.1')].items():
                                     if k != key1 and k not in k2:
+                                        new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0]
                                         if len(add_mut23) == 0:
-                                            add_mut23 = str(k) + "_" + v
+                                            add_mut23 = new_mut
                                         else:
-                                            add_mut23 = add_mut23 + ", " + str(k) + "_" + v
+                                            add_mut23 = add_mut23 + ", " + new_mut
                     else:
                         total3 = total3new = na3 = lowq3 = 0
                         ref3 = alt3 = ref3f = alt3f = 0
@@ -441,10 +444,11 @@
                             if add_mut4 > 1:
                                 for k, v in mut_read_dict[(key2[:-5] + '.ba.2')].items():
                                     if k != key1 and k not in k1:
+                                        new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0]
                                         if len(add_mut14) == 0:
-                                            add_mut14 = str(k) + "_" + v
+                                            add_mut14 = new_mut
                                         else:
-                                            add_mut14 = add_mut14 + ", " + str(k) + "_" + v
+                                            add_mut14 = add_mut14 + ", " + new_mut
                     else:
                         total4 = total4new = na4 = lowq4 = 0
                         ref4 = alt4 = ref4f = alt4f = 0
diff -r 4fc62ab6e9e8 -r 386438cd4c3b read2mut.xml
--- a/read2mut.xml	Sat Oct 17 09:11:53 2020 +0000
+++ b/read2mut.xml	Tue Oct 27 12:39:21 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.4" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.5" profile="19.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>