From acdea352102b176dc519f6cbdd7980d1041079c2 Mon Sep 17 00:00:00 2001
From: Derek <derekwbarnett@gmail.com>
Date: Tue, 17 Aug 2010 21:51:51 -0400
Subject: [PATCH] Minor formatting cleanup in BamIndex.*

---
 BamIndex.cpp | 8 +++++---
 BamIndex.h   | 5 ++++-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/BamIndex.cpp b/BamIndex.cpp
index 787995b..d74e751 100644
--- a/BamIndex.cpp
+++ b/BamIndex.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 13 July 2010 (DB)
+// Last modified: 17 August 2010 (DB)
 // ---------------------------------------------------------------------------
 // Provides index functionality - both for the default (standardized) BAM 
 // index format (.bai) as well as a BamTools-specific (nonstandard) index 
@@ -13,7 +13,7 @@
 #include <cstdio>
 #include <cstdlib>
 #include <algorithm>
-#include <iostream>
+// #include <iostream>
 #include <map>
 #include "BamIndex.h"
 #include "BamReader.h"
@@ -52,6 +52,8 @@ bool BamIndex::HasAlignments(const int& referenceID) {
  
 namespace BamTools { 
 
+// --------------------------------------------------
+// BamDefaultIndex data structures & typedefs
 struct Chunk {
 
     // data members
@@ -88,7 +90,7 @@ struct ReferenceIndex {
     { }
 };
 
-typedef vector<ReferenceIndex> BamDefaultIndexData;  
+typedef vector<ReferenceIndex> BamDefaultIndexData;
 
 } // namespace BamTools
  
diff --git a/BamIndex.h b/BamIndex.h
index aeecefb..b9ce7d0 100644
--- a/BamIndex.h
+++ b/BamIndex.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 13 July 2010 (DB)
+// Last modified: 17 August 2010 (DB)
 // ---------------------------------------------------------------------------
 // Provides index functionality - both for the default (standardized) BAM 
 // index format (.bai) as well as a BamTools-specific (nonstandard) index 
@@ -22,6 +22,7 @@ namespace BamTools {
 class BamReader;
 class BgzfData;
   
+// --------------------------------------------------  
 // BamIndex base class
 class BamIndex {
 
@@ -51,6 +52,7 @@ class BamIndex {
         bool m_isBigEndian;
 };
 
+// --------------------------------------------------
 // BamDefaultIndex class
 // 
 // implements default (per SAM/BAM spec) index file ops
@@ -82,6 +84,7 @@ class BamDefaultIndex : public BamIndex {
         BamDefaultIndexPrivate* d;
 };
 
+// --------------------------------------------------
 // BamToolsIndex class
 //
 // implements BamTools-specific index file ops
-- 
2.39.2