allow to exclude MSA sites from the analysis (#189)

1. Partition file now supports comment lines such that individual partitions can be easily excluded, e.g.

```
 LG+G, p1 = 1-20, 81-113
 #disable partition p2
 #WAG+G, p2 = 21-50
 JTT, p3 = 51-70
```

2. To prevent excluding MSA sites by mistake, you need to add `--force msa_extra_cols` to explicitely disable partition completeness check

src/PartitionedMSA.cpp

@@ -16,6 +16,7 @@ PartitionedMSA& PartitionedMSA::operator=(PartitionedMSA&& other)
   _full_msa = std::move(other._full_msa);
   _taxon_names = std::move(other._taxon_names);
   _taxon_id_map = std::move(other._taxon_id_map);
+  _unassigned_sites = std::move(other._unassigned_sites);
   _subst_linkage = std::move(other._subst_linkage);
   _freqs_linkage = std::move(other._freqs_linkage);
    return *this;
@@ -64,17 +65,15 @@ uintVector PartitionedMSA::get_site_part_assignment() const
     p++;
   }
 
+  assert(p == part_count());
+
   /* check if all sites were assigned to partitions */
-  MissingPartitionForSiteException e_unassinged;
   for (size_t i = 0; i < full_len; ++i)
   {
     if (!spa[i])
-      e_unassinged.add_unassigned_site(i+1);
+      _unassigned_sites.push_back(i+1);
   }
 
-  if (e_unassinged.count() > 0)
-    throw e_unassinged;
-
   return spa;
 }
 

src/PartitionedMSA.hpp

@@ -25,6 +25,7 @@ class PartitionedMSA
   std::vector<PartitionInfo>& part_list() { return _part_list; };
   const NameList& taxon_names()  const { return _taxon_names; };
   const NameIdMap& taxon_id_map() const { return _taxon_id_map; }
+  const IDVector& unassigned_sites()  const { return _unassigned_sites; };
 
   size_t full_msa_site(size_t index, size_t site) const;
   const uintVector& site_part_map() const;
@@ -41,6 +42,7 @@ class PartitionedMSA
   /* given in elements (NOT in bytes) */
   size_t taxon_clv_size() const;
 
+
   // setters
   void full_msa(MSA&& msa);
   void part_msa(size_t index, MSA&& msa) { _part_list.at(index).msa(std::move(msa)); };
@@ -82,6 +84,7 @@ class PartitionedMSA
   NameList _taxon_names;
   NameIdMap _taxon_id_map;
   mutable uintVector _site_part_map;
+  mutable IDVector _unassigned_sites;
   double _difficulty_score;
   uintVector _subst_linkage;
   uintVector _freqs_linkage;

src/io/part_info.cpp

@@ -28,6 +28,11 @@ RaxmlPartitionStream& operator>>(RaxmlPartitionStream& stream, PartitionInfo& pa
       case '\t':
         /* ignore whitespace */
         break;
+      case '#':
+        /* comment: ignore line */
+        while (stream.peek() != '\n' && stream.peek() != EOF)
+          stream.get();
+        break;
       case '\r':
         /* handle Windows line breaks (\r\n) */
         if (stream.peek() == '\n')

src/main.cpp

@@ -415,6 +415,37 @@ bool check_msa(RaxmlInstance& instance)
     msa_valid &= parted_msa_view.taxon_name_map().empty();
   }
 
+  if (!parted_msa.unassigned_sites().empty())
+  {
+    auto extra_sites = parted_msa.unassigned_sites();
+    if (opts.safety_checks.isset(SafetyCheck::msa_extra_cols))
+    {
+      LOG_ERROR << "\nERROR: Found " << extra_sites.size() <<
+          " alignment site(s) which are not assigned to any partition:" << endl;
+
+      for (size_t i = 0; i < extra_sites.size(); ++i)
+      {
+        LOG_ERROR << extra_sites[i] << " ";
+        if (i >= 1000)
+        {
+          LOG_ERROR << "...";
+          break;
+        }
+      }
+
+      LOG_ERROR << "\nNOTE:  If you want to ignore these sites, "
+          "please add '--force msa_extra_cols' option." << endl;
+
+      msa_valid = false;
+    }
+    else
+    {
+      LOG_WARN << "\nWARNING: Found " << extra_sites.size() <<
+          " alignment site(s) which are not assigned to any partition."
+          " They will be ignored." << endl;
+    }
+  }
+
   /* check for duplicate sequences */
   if (opts.safety_checks.isset(SafetyCheck::msa_dups))
   {

src/util/SafetyCheck.cpp

@@ -17,6 +17,8 @@ SafetyCheck::Flags SafetyCheck::from_string(const string& s)
     return SafetyCheck::msa_dups;
   else if (s == "msa_allgaps")
     return SafetyCheck::msa_allgaps;
+  else if (s == "msa_extra_cols")
+    return SafetyCheck::msa_extra_cols;
   else if (s == "model")
     return SafetyCheck::model;
   else if (s == "model_zero_freqs")

src/util/SafetyCheck.hpp

@@ -17,7 +17,8 @@ struct SafetyCheck
     msa_names            = 1 << 10,
     msa_dups             = 1 << 11,
     msa_allgaps          = 1 << 12,
-    msa                  = msa_names | msa_dups | msa_allgaps,
+    msa_extra_cols       = 1 << 13,
+    msa                  = msa_names | msa_dups | msa_allgaps | msa_extra_cols,
     model_zero_freqs     = 1 << 21,
     model_invalid_freqs  = 1 << 22,
     model_lg4_freqs      = 1 << 23,

src/version.h

@@ -1,3 +1,3 @@
 #define RAXML_VERSION "2.0.0-dev"
-#define RAXML_DATE    "15.01.2025"
+#define RAXML_DATE    "17.01.2025"
 #define RAXML_INTVER  200