From: Michael R. Crusoe <crusoe@ucdavis.edu>
Subject: fixes a couple Doxygen warnings
Forwarded: https://github.com/pezmaster31/bamtools/pull/120

--- bamtools.orig/src/api/BamMultiReader.cpp
+++ bamtools/src/api/BamMultiReader.cpp
@@ -361,10 +361,10 @@
     method can be useful when you know, for example, that your BAM files are sorted
     by coordinate but upstream processes did not set the header tag properly.
 
-    \note This method should \bold not be called while reading alignments via
+    \note This method should \b not be called while reading alignments via
     GetNextAlignment() or GetNextAlignmentCore(). For proper results, you should
     call this method before (or immediately after) opening files, rewinding,
-    jumping, etc. but \bold not once alignment fetching has started. There is
+    jumping, etc. but \b not once alignment fetching has started. There is
     nothing in the API to prevent you from doing so, but the results may be
     unexpected.
 
--- bamtools.orig/docs/Doxyfile
+++ bamtools/docs/Doxyfile
@@ -1454,7 +1454,7 @@
 # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
 # containing the font.
 
-DOT_FONTNAME           = FreeSans
+# DOT_FONTNAME           = FreeSans
 
 # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
 # The default size is 10pt.
--- bamtools.orig/src/api/BamAlignment.h
+++ bamtools/src/api/BamAlignment.h
@@ -143,12 +143,13 @@
         bool SkipToNextTag(const char storageType,
                            char*& pTagData,
                            unsigned int& numBytesParsed) const;
-
+    //! \internal
     // internal data
     private:
 
         struct BamAlignmentSupportData {
-      
+
+            //! \internal
             // data members
             std::string AllCharData;
             uint32_t    BlockLength;
@@ -156,7 +157,8 @@
             uint32_t    QueryNameLength;
             uint32_t    QuerySequenceLength;
             bool        HasCoreOnly;
-            
+
+	    //! \internal
             // constructor
             BamAlignmentSupportData(void)
                 : BlockLength(0)
@@ -171,7 +173,6 @@
         friend class Internal::BamWriterPrivate;
 
         mutable std::string ErrorString; // mutable to allow updates even in logically const methods
-    //! \endinternal
 };
 
 // ---------------------------------------------------------
