undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.44.af89940 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.45.71ca9cd #_#UPDATE_VERSION -- Populated by edit_version.pl
 The version ID is organized as follows: <Major Release>.<Latest Stable>.<Latest Beta>.<Github version tag>
 Content of this directory: 
 Linux Installation:

docs/.html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c8aac10e88e8ff4892edf17a9b14a7b1
+config: 755d780570ae6ddba6c572e3b81e9688
 tags: 33eac41acc08762151beb8f3b7b86c8f

docs/.html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'Version_13.45.44.af89940',
+    VERSION: 'Version_13.45.45.71ca9cd',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/.html/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.44.af89940 documentation</title>
+  <title>T-Coffee Version_13.45.45.71ca9cd documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.44.af89940
+                Version_13.45.45.71ca9cd
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.44.af89940 documentation</li>
+      <li>T-Coffee Version_13.45.45.71ca9cd documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.44.af89940' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.45.71ca9cd' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.44.af89940' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.45.71ca9cd' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

lib/io_lib/tree_util.c

@@ -8189,7 +8189,7 @@ ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq)
   ALNcol**graph=(ALNcol**)vcalloc ( A->len_aln, sizeof (ALNcol*));
   ALNcol *lp, *p, *test;
   ALNcol *start, *end, *parent, *child, *lchild, *lparent;
-  int compact=-1;
+  int compact=0;
   int check_homoplasy=1;
   int *rescount;
   int *gapcount;
@@ -8273,7 +8273,7 @@ ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq)
 	  start=(S2[seq][r])->next;
 	  end  =(S2[seq][r+1]);
 	  g=re=0;
-	  while (start!=end)
+	  while (start && start!=end)
 	    {
 	      g+=start->ngap;
 	      re+=start->nres;
@@ -8325,7 +8325,6 @@ ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq)
 
   if (!msa)//graph gets turned into msa
     {
-
       msa=start=declare_alncol();
       end=declare_alncol();
       start->aa=-1;
@@ -8335,62 +8334,63 @@ ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq)
       for (c=0; c<A->len_aln; c++)
 	{
 	  graph[c]->next=(c<A->len_aln-1)?graph[c+1]:end;
-	}
-
+  	}
     }
-   else if (compact == 0)//concatenate 
+  else if ( compact ==1)//stack
     {
-      //Insert graph into msa by expanding seq
-      //Trick: graph[A->len_aln] contains all the nodes
-      //the ones from seq are already in. They can be recognised with aa==1
-      //the new ones are the gaps and they need to be connected to the aa==1
-
+      //Same as above but stack positions gapped between the same pair of residues in the guide sequence
       ALNcol*last=msa;
 
       for (c=0; c<S->len[seq]; c++)(S2[seq][c])->aa=1;
       for (c=0; c<A->len_aln; c++)
 	{
 	  if (graph[c]->aa)last=graph[c];
-	  else 
+	  else if (last->next && !(last->next)->aa)
+	    {
+	      for ( s=0; s<A->nseq; s++)
+		{
+		  int ir=pos[s][c];
+		  if (ir!=-1 && S2[lu[s]][ir])S2[lu[s]][ir]=last;
+		}
+	      last=last->next;
+	    }
+	  else
 	    {
-	      //This is where new columns of gaps are inserted in the MSA
 	      graph[c]->next=last->next;
-	      last->next=graph[c];
+	      last->next= graph[c];
 	      last=last->next;
 	    }
 	}
       for (c=0; c<S->len[seq]; c++)(S2[seq][c])->aa=0;
     }
-   else if ( compact ==1)//stack
+  else if ( compact==-1)
     {
-      //Same as above but stack positions gapped between the same pair of residues in the guide sequence
+      HERE ("WARNING MSAs not being properly combined");
+    }
+  else
+    {
+      //Insert graph into msa by expanding seq
+      //Trick: graph[A->len_aln] contains all the nodes
+      //the ones from seq are already in. They can be recognised with aa==1
+      //the new ones are the gaps and they need to be connected to the aa==1
+      //This is the mode that was used in the NAture Biotech
       ALNcol*last=msa;
 
       for (c=0; c<S->len[seq]; c++)(S2[seq][c])->aa=1;
       for (c=0; c<A->len_aln; c++)
 	{
 	  if (graph[c]->aa)last=graph[c];
-	  else if (last->next && !(last->next)->aa)
-	    {
-	      for ( s=0; s<A->nseq; s++)
-		{
-		  int ir=pos[s][c];
-		  if (ir!=-1 && S2[lu[s]][ir])S2[lu[s]][ir]=last;
-		}
-	      last=last->next;
-	    }
-	  else
+	  else 
 	    {
+	      //This is where new columns of gaps are inserted in the MSA
 	      graph[c]->next=last->next;
-	      last->next= graph[c];
+	      last->next=graph[c];
 	      last=last->next;
 	    }
 	}
       for (c=0; c<S->len[seq]; c++)(S2[seq][c])->aa=0;
     }
 
-
-
 
   //This assigns an index to every column in the linked list MSA
 

lib/perl/lib/scripts/dynamic.pl

@@ -220,13 +220,13 @@
 $threadFlag4famsa=($thread)?"-t $thread ":"-t 1 ";
 $CL4tc.=" $threadFlag4tc ";
 
-print "\n![dynamic.pl] --- CL4tc == $CL4tc\n";  
+if ($VERBOSE){print "\n![dynamic.pl] --- CL4tc == $CL4tc\n";}
 
 my $cmethod=$method2use;
 $cmethod=~s/_pair/_msa/;
 $cmethod=~s/_msa//;
 
-print "\n![dynamic.pl] --- cmethod == $cmethod\n";  
+if ($VERBOSE){print "\n![dynamic.pl] --- cmethod == $cmethod\n";}
 
 if ($cmethod eq "tcoffee"|| $cmethod eq "t_coffee" )
   {

lib/version/build_version.version

@@ -1 +1 @@
-44
+45

lib/version/github.version

@@ -1 +1 @@
-* master af89940 undocumented beta release tested with beta tests
+* master 71ca9cd undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.44.af89940
+Version_13.45.45.71ca9cd