Brought API up to compliance with recent SAM Format Spec (v1.4-r962)

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

diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index 6a97980b400298593733a370cb91239de8d2c4a6..e433c8e79df37d318a6f4a9c7b94b060494b9a92 100644 (file)
--- a/src/api/BamConstants.h
+++ b/src/api/BamConstants.h
@@ -1,10 +1,20 @@
+// ***************************************************************************
+// BamConstants.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 April 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides basic constants for handling BAM files.
+// ***************************************************************************
+
 #ifndef BAM_CONSTANTS_H
 #define BAM_CONSTANTS_H
 
 #include <string>
 
 /*! \namespace BamTools::Constants
-    \brief Contains most of the constants used throughout BamTools.
+    \brief Provides basic constants for handling BAM files.
 */
 
 namespace BamTools {
@@ -21,20 +31,20 @@ const int BAM_CORE_SIZE = 32;
 const int BAM_CORE_BUFFER_SIZE = 8;
 
 // BAM alignment flags
-const int BAM_ALIGNMENT_PAIRED              = 1;
-const int BAM_ALIGNMENT_PROPER_PAIR         = 2;
-const int BAM_ALIGNMENT_UNMAPPED            = 4;
-const int BAM_ALIGNMENT_MATE_UNMAPPED       = 8;
-const int BAM_ALIGNMENT_REVERSE_STRAND      = 16;
-const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 32;
-const int BAM_ALIGNMENT_READ_1              = 64;
-const int BAM_ALIGNMENT_READ_2              = 128;
-const int BAM_ALIGNMENT_SECONDARY           = 256;
-const int BAM_ALIGNMENT_QC_FAILED           = 512;
-const int BAM_ALIGNMENT_DUPLICATE           = 1024;
+const int BAM_ALIGNMENT_PAIRED              = 0x0001;
+const int BAM_ALIGNMENT_PROPER_PAIR         = 0x0002;
+const int BAM_ALIGNMENT_UNMAPPED            = 0x0004;
+const int BAM_ALIGNMENT_MATE_UNMAPPED       = 0x0008;
+const int BAM_ALIGNMENT_REVERSE_STRAND      = 0x0010;
+const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
+const int BAM_ALIGNMENT_READ_1              = 0x0040;
+const int BAM_ALIGNMENT_READ_2              = 0x0080;
+const int BAM_ALIGNMENT_SECONDARY           = 0x0100;
+const int BAM_ALIGNMENT_QC_FAILED           = 0x0200;
+const int BAM_ALIGNMENT_DUPLICATE           = 0x0400;
 
 // CIGAR constants
-const char* const BAM_CIGAR_LOOKUP = "MIDNSHP";
+const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
 const int BAM_CIGAR_MATCH    = 0;
 const int BAM_CIGAR_INS      = 1;
 const int BAM_CIGAR_DEL      = 2;
@@ -42,6 +52,8 @@ const int BAM_CIGAR_REFSKIP  = 3;
 const int BAM_CIGAR_SOFTCLIP = 4;
 const int BAM_CIGAR_HARDCLIP = 5;
 const int BAM_CIGAR_PAD      = 6;
+const int BAM_CIGAR_SEQMATCH = 7;
+const int BAM_CIGAR_MISMATCH = 8;
 
 const char BAM_CIGAR_MATCH_CHAR    = 'M';
 const char BAM_CIGAR_INS_CHAR      = 'I';
@@ -50,6 +62,8 @@ const char BAM_CIGAR_REFSKIP_CHAR  = 'N';
 const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
 const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
 const char BAM_CIGAR_PAD_CHAR      = 'P';
+const char BAM_CIGAR_SEQMATCH_CHAR = '=';
+const char BAM_CIGAR_MISMATCH_CHAR = 'X';
 
 const int BAM_CIGAR_SHIFT    = 4;
 const int BAM_CIGAR_MASK     = ((1 << BAM_CIGAR_SHIFT) - 1);
@@ -65,9 +79,11 @@ const char BAM_TAG_TYPE_INT32  = 'I';
 const char BAM_TAG_TYPE_FLOAT  = 'f';
 const char BAM_TAG_TYPE_STRING = 'Z';
 const char BAM_TAG_TYPE_HEX    = 'H';
+const char BAM_TAG_TYPE_ARRAY  = 'B';
 
 const size_t BAM_TAG_TAGSIZE  = 2;
 const size_t BAM_TAG_TYPESIZE = 1;
+const int BAM_TAG_ARRAYBASE_SIZE = 8;
 
 // DNA bases
 const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";