Regression fixed: error in BamAlignment tag access methods

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

diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index f1af90d5573d3b19f92a10f14613ff54316e2293..47f73a9baf3161db336dbe0dc66343f3ef147cee 100644 (file)
--- a/src/api/BamConstants.h
+++ b/src/api/BamConstants.h
@@ -2,7 +2,7 @@
 // BamConstants.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 16 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides basic constants for handling BAM files.
 // ***************************************************************************
@@ -10,7 +10,7 @@
 #ifndef BAM_CONSTANTS_H
 #define BAM_CONSTANTS_H
 
-#include <api/api_global.h>
+#include "api/api_global.h"
 #include <cassert>
 #include <string>
 
@@ -69,14 +69,14 @@ const char BAM_CIGAR_MISMATCH_CHAR = 'X';
 const int BAM_CIGAR_SHIFT = 4;
 const int BAM_CIGAR_MASK  = ((1 << BAM_CIGAR_SHIFT) - 1);
 
-// BAM tag types
+// BAM tag types & sizes
 const char BAM_TAG_TYPE_ASCII  = 'A';
-const char BAM_TAG_TYPE_UINT8  = 'c';
-const char BAM_TAG_TYPE_INT8   = 'C';
-const char BAM_TAG_TYPE_UINT16 = 's';
-const char BAM_TAG_TYPE_INT16  = 'S';
-const char BAM_TAG_TYPE_UINT32 = 'i';
-const char BAM_TAG_TYPE_INT32  = 'I';
+const char BAM_TAG_TYPE_INT8   = 'c';
+const char BAM_TAG_TYPE_UINT8  = 'C';
+const char BAM_TAG_TYPE_INT16  = 's';
+const char BAM_TAG_TYPE_UINT16 = 'S';
+const char BAM_TAG_TYPE_INT32  = 'i';
+const char BAM_TAG_TYPE_UINT32 = 'I';
 const char BAM_TAG_TYPE_FLOAT  = 'f';
 const char BAM_TAG_TYPE_STRING = 'Z';
 const char BAM_TAG_TYPE_HEX    = 'H';
@@ -124,7 +124,7 @@ const char BAM_DNA_N     = 'N';
 const char BAM_DNA_DEL   = '-';
 const char BAM_DNA_PAD   = '*';
 
-// zlib constants
+// zlib & BGZF constants
 const char GZIP_ID1   = 31;
 const char GZIP_ID2   = 139;
 const char CM_DEFLATE = 8;
@@ -134,10 +134,9 @@ const char BGZF_XLEN  = 6;
 const char BGZF_ID1   = 66;
 const char BGZF_ID2   = 67;
 const char BGZF_LEN   = 2;
-const int8_t GZIP_WINDOW_BITS = -15;
-const int8_t Z_DEFAULT_MEM_LEVEL = 8;
 
-// BZGF constants
+const int8_t   GZIP_WINDOW_BITS          = -15;
+const int8_t   Z_DEFAULT_MEM_LEVEL       = 8;
 const uint8_t  BGZF_BLOCK_HEADER_LENGTH  = 18;
 const uint8_t  BGZF_BLOCK_FOOTER_LENGTH  = 8;
 const uint32_t BGZF_MAX_BLOCK_SIZE       = 65536;
@@ -145,6 +144,7 @@ const uint32_t BGZF_DEFAULT_BLOCK_SIZE   = 65536;
 
 } // namespace Constants
 
+//! \cond
 // -------------------------
 // tag-type helper structs
 // -------------------------
@@ -190,7 +190,7 @@ struct TagTypeHelper<int8_t> {
 
 template<>
 struct TagTypeHelper<uint16_t> {
-    static bool CanCovnertFrom(const char c) {
+    static bool CanConvertFrom(const char c) {
         return ( c == Constants::BAM_TAG_TYPE_ASCII ||
                  c == Constants::BAM_TAG_TYPE_UINT8 ||
                  c == Constants::BAM_TAG_TYPE_UINT16 );
@@ -275,6 +275,8 @@ struct TagTypeHelper<std::string> {
     static char TypeCode(void) { return Constants::BAM_TAG_TYPE_STRING; }
 };
 
+//! \endcond
+
 } // namespace BamTools
 
 #endif // BAM_CONSTANTS_H