Changeset 3477 for trunk/yat/omic/BamHeader.cc

Timestamp:

Mar 9, 2016, 9:26:38 AM (7 years ago)

Author:

Peter

Message:

add functionality to access which RG IDs that are present in a BamHeader?

File:

• trunk/yat/omic/BamHeader.cc (modified) (3 diffs)

trunk/yat/omic/BamHeader.cc

@@ -81 +81 @@
                                       const std::string& id,
                                       const std::string& key) const
+  {
+    update_group(table, type);
+    strMap2::const_iterator line_table = table.find(id);
+    if (line_table == table.end()) {
+      std::string msg = "@" + type + ": unknown ID: '" + id + "'";
+      throw utility::runtime_error(msg);
+    }
+    strMap::const_iterator it = line_table->second.find(key);
+    if (it == line_table->second.end()) {
+      std::string msg = "@" + type + ": unknown KEY: '" + key + "'";
+      throw utility::runtime_error(msg);
+    }
+    return it->second;
+  }
+
+
+  void BamHeader::update_group(strMap2& table, const std::string& type) const
   {
     assert(type.size()==2);
@@ -101 +118 @@
       }
     }
-    strMap2::const_iterator line_table = table.find(id);
-    if (line_table == table.end()) {
-      std::string msg = "@" + type + ": unknown ID: '" + id + "'";
-      throw utility::runtime_error(msg);
-    }
-    strMap::const_iterator it = line_table->second.find(key);
-    if (it == line_table->second.end()) {
-      std::string msg = "@" + type + ": unknown KEY: '" + key + "'";
-      throw utility::runtime_error(msg);
-    }
-    return it->second;
   }
 
@@ -156 +162 @@
   {
     return group(read_group_, "RG", id, key);
+  }
+
+
+  const std::map<std::string, std::string>&
+  BamHeader::read_group(const std::string& id) const
+  {
+    update_group(read_group_, "RG");
+    strMap2::const_iterator line_table = read_group_.find(id);
+    if (line_table == read_group_.end()) {
+      std::string msg = "@RG: unknown ID: '" + id + "'";
+      throw utility::runtime_error(msg);
+    }
+    return line_table->second;
+  }
+
+
+  BamHeader::read_group_iterator BamHeader::read_group_begin(void) const
+  {
+    update_group(read_group_, "RG");
+    BamHeader::strMap2::const_iterator it(read_group_.begin());
+    return utility::pair_first_iterator(it);
+  }
+
+
+  BamHeader::read_group_iterator BamHeader::read_group_end(void) const
+  {
+    update_group(read_group_, "RG");
+    BamHeader::strMap2::const_iterator it(read_group_.end());
+    return utility::pair_first_iterator(it);
   }