From: Derek <derekwbarnett@gmail.com>
Date: Thu, 16 Sep 2010 05:47:58 +0000 (-0400)
Subject: Did some housekeeping in BamAux.h - moved some constants to the files where they... 
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e9617e555c77b5b58da1959e18e6421fa5f271a9;p=bamtools.git

Did some housekeeping in BamAux.h - moved some constants to the files where they are actually used.
---

diff --git a/src/api/BamAux.h b/src/api/BamAux.h
index a122b24..daad5a0 100644
--- a/src/api/BamAux.h
+++ b/src/api/BamAux.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 15 September 2010 (DB)
+// Last modified: 16 September 2010 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic constants, data structures, etc. for using BAM files
 // ***************************************************************************
@@ -46,24 +46,9 @@
 namespace BamTools {
 
 // BAM constants
-const int BAM_CORE_SIZE   = 32;
-const int BAM_CMATCH      = 0;
-const int BAM_CINS        = 1;
-const int BAM_CDEL        = 2;
-const int BAM_CREF_SKIP   = 3;
-const int BAM_CSOFT_CLIP  = 4;
-const int BAM_CHARD_CLIP  = 5;
-const int BAM_CPAD        = 6;
 const int BAM_CIGAR_SHIFT = 4;
 const int BAM_CIGAR_MASK  = ((1 << BAM_CIGAR_SHIFT) - 1);
-
-// BAM index constants
-const int MAX_BIN           = 37450;	// =(8^6-1)/7+1
-const int BAM_MIN_CHUNK_GAP = 32768;
-const int BAM_LIDX_SHIFT    = 14;
-
-// Explicit variable sizes
-const int BT_SIZEOF_INT = 4;
+const int BAM_CORE_SIZE   = 32;
 
 struct CigarOp;
 
diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp
index c628b79..a7f93de 100644
--- a/src/api/BamIndex.cpp
+++ b/src/api/BamIndex.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 10 September 2010 (DB)
+// Last modified: 16 September 2010 (DB)
 // ---------------------------------------------------------------------------
 // Provides index functionality - both for the default (standardized) BAM 
 // index format (.bai) as well as a BamTools-specific (nonstandard) index 
@@ -52,6 +52,10 @@ bool BamIndex::HasAlignments(const int& referenceID) {
  
 namespace BamTools { 
 
+// BAM index constants
+const int MAX_BIN           = 37450;    // =(8^6-1)/7+1
+const int BAM_LIDX_SHIFT    = 14;  
+  
 // --------------------------------------------------
 // BamStandardIndex data structures & typedefs
 struct Chunk {
diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp
index 2be38bb..c3c94ef 100644
--- a/src/api/BamWriter.cpp
+++ b/src/api/BamWriter.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 17 August 2010 (DB)
+// Last modified: 16 September 2010 (DB)
 // ---------------------------------------------------------------------------
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -18,6 +18,20 @@
 using namespace BamTools;
 using namespace std;
 
+namespace BamTools {
+
+// BAM constants
+const int BT_SIZEOF_INT   = 4;
+const int BAM_CMATCH      = 0;
+const int BAM_CINS        = 1;
+const int BAM_CDEL        = 2;
+const int BAM_CREF_SKIP   = 3;
+const int BAM_CSOFT_CLIP  = 4;
+const int BAM_CHARD_CLIP  = 5;
+const int BAM_CPAD        = 6;
+
+} // namespace BamTools
+
 struct BamWriter::BamWriterPrivate {
 
     // data members