Minor formatting cleanup

[bamtools.git] / src / api / BamReader.h

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 7bdcbe7ace9da6e0f7f23eb072d91fa69a132f5b..c3452f6cb82b34c95596e68f9d673d41af051e9b 100644 (file)
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -44,9 +44,9 @@ class API_EXPORT BamReader {
         bool Jump(int refID, int position = 0);\r
         // opens BAM file (and optional BAM index file, if provided)\r
         // @lookForIndex - if no indexFilename provided, look in BAM file's directory for an existing index file\r
-       //   default behavior is to skip index file search if no index filename given\r
+        //   default behavior is to skip index file search if no index filename given\r
         // @preferStandardIndex - if true, give priority in index file searching to standard BAM index (*.bai)\r
-       //   default behavior is to prefer the BamToolsIndex (*.bti) if both are available\r
+        //   default behavior is to prefer the BamToolsIndex (*.bti) if both are available\r
         bool Open(const std::string& filename, \r
                   const std::string& indexFilename = "", \r
                   const bool lookForIndex = false, \r
@@ -67,7 +67,7 @@ class API_EXPORT BamReader {
         // retrieves next available alignment core data (returns success/fail)\r
         // ** DOES NOT parse any character data (read name, bases, qualities, tag data) **\r
         // useful for operations requiring ONLY aligner-related information \r
-       // (refId/position, alignment flags, CIGAR, mapQuality, etc)\r
+        // (refId/position, alignment flags, CIGAR, mapQuality, etc)\r
         bool GetNextAlignmentCore(BamAlignment& bAlignment);\r
 \r
         // ----------------------\r
@@ -93,36 +93,36 @@ class API_EXPORT BamReader {
         // default behavior is to create the BAM standard index (".bai")\r
         // set flag to false to create the BamTools-specific index (".bti")\r
         bool CreateIndex(bool useStandardIndex = true);\r
-       // returns whether index data is available for reading \r
-       // (e.g. if true, BamReader should be able to seek to a region)\r
-       bool HasIndex(void) const;\r
-       // change the index caching behavior\r
-       // default BamReader/Index mode is LimitedIndexCaching\r
-       // @mode - can be either FullIndexCaching, LimitedIndexCaching, \r
-       //   or NoIndexCaching. See BamIndex.h for more details\r
+        // returns whether index data is available for reading\r
+        // (e.g. if true, BamReader should be able to seek to a region)\r
+        bool HasIndex(void) const;\r
+        // change the index caching behavior\r
+        // default BamReader/Index mode is LimitedIndexCaching\r
+        // @mode - can be either FullIndexCaching, LimitedIndexCaching,\r
+        //   or NoIndexCaching. See BamIndex.h for more details\r
         void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);\r
        \r
     // deprecated methods\r
     public:\r
        \r
-       // deprecated (but still available): prefer HasIndex() instead\r
-       //\r
-       // Deprecated purely for API semantic clarity - HasIndex() should be clearer \r
-       // than IsIndexLoaded() in light of the new caching modes that may clear the \r
-       // index data from memory, but leave the index file open for later random access \r
-       // seeks.\r
-       //\r
-       // For example, what would (IsIndexLoaded() == true) mean when cacheMode has been \r
-       // explicitly set to NoIndexCaching? This is confusing at best, misleading about \r
-       // current memory behavior at worst.\r
-       //\r
-       // returns whether index data is available \r
-       // (e.g. if true, BamReader should be able to seek to a region)\r
+        // deprecated (but still available): prefer HasIndex() instead\r
+        //\r
+        // Deprecated purely for API semantic clarity - HasIndex() should be clearer\r
+        // than IsIndexLoaded() in light of the new caching modes that may clear the\r
+        // index data from memory, but leave the index file open for later random access\r
+        // seeks.\r
+        //\r
+        // For example, what would (IsIndexLoaded() == true) mean when cacheMode has been\r
+        // explicitly set to NoIndexCaching? This is confusing at best, misleading about\r
+        // current memory behavior at worst.\r
+        //\r
+        // returns whether index data is available\r
+        // (e.g. if true, BamReader should be able to seek to a region)\r
         bool IsIndexLoaded(void) const;\r
         \r
     // private implementation\r
     private:\r
-       Internal::BamReaderPrivate* d;\r
+        Internal::BamReaderPrivate* d;\r
 };\r
 \r
 } // namespace BamTools\r