Fixed: sorting order lost during merge step of sort tool, if input BAM

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

diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h
index 6412b3d0bce6bb9eefcbb205352cfaae0e4b3013..4bb7ee9b0268a392dec65ca1ee8fd64965912322 100644 (file)
--- a/src/api/SamConstants.h
+++ b/src/api/SamConstants.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // SamConstants.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 23 December 2010 (DB)
+// Last modified: 27 March 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides constants for SAM header
 // ***************************************************************************
@@ -11,12 +10,13 @@
 #ifndef SAM_CONSTANTS_H
 #define SAM_CONSTANTS_H
 
-#include <api/api_global.h>
+#include "api/api_global.h"
 #include <string>
 
 namespace BamTools {
 namespace Constants {
 
+// basic char constants used in SAM format
 const char SAM_COLON  = ':';
 const char SAM_EQUAL  = '=';
 const char SAM_PERIOD = '.';
@@ -24,6 +24,8 @@ const char SAM_STAR   = '*';
 const char SAM_TAB    = '\t';
 const std::string SAM_DIGITS = "0123456789";
 
+const std::string SAM_CURRENT_VERSION = "1.4";
+
 // HD entries
 const std::string SAM_HD_BEGIN_TOKEN    = "@HD";
 const std::string SAM_HD_VERSION_TAG    = "VN";
@@ -32,30 +34,35 @@ const std::string SAM_HD_GROUPORDER_TAG = "GO";
 
 // SQ entries
 const std::string SAM_SQ_BEGIN_TOKEN    = "@SQ";
-const std::string SAM_SQ_NAME_TAG       = "SN";
-const std::string SAM_SQ_LENGTH_TAG     = "LN";
 const std::string SAM_SQ_ASSEMBLYID_TAG = "AS";
-const std::string SAM_SQ_URI_TAG        = "UR";
 const std::string SAM_SQ_CHECKSUM_TAG   = "M5";
+const std::string SAM_SQ_LENGTH_TAG     = "LN";
+const std::string SAM_SQ_NAME_TAG       = "SN";
 const std::string SAM_SQ_SPECIES_TAG    = "SP";
+const std::string SAM_SQ_URI_TAG        = "UR";
 
 // RG entries
 const std::string SAM_RG_BEGIN_TOKEN             = "@RG";
+const std::string SAM_RG_DESCRIPTION_TAG         = "DS";
+const std::string SAM_RG_FLOWORDER_TAG           = "FO";
 const std::string SAM_RG_ID_TAG                  = "ID";
-const std::string SAM_RG_SAMPLE_TAG              = "SM";
+const std::string SAM_RG_KEYSEQUENCE_TAG         = "KS";
 const std::string SAM_RG_LIBRARY_TAG             = "LB";
-const std::string SAM_RG_DESCRIPTION_TAG         = "DS";
 const std::string SAM_RG_PLATFORMUNIT_TAG        = "PU";
 const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI";
-const std::string SAM_RG_SEQCENTER_TAG           = "CN";
 const std::string SAM_RG_PRODUCTIONDATE_TAG      = "DT";
+const std::string SAM_RG_PROGRAM_TAG             = "PG";
+const std::string SAM_RG_SAMPLE_TAG              = "SM";
+const std::string SAM_RG_SEQCENTER_TAG           = "CN";
 const std::string SAM_RG_SEQTECHNOLOGY_TAG       = "PL";
 
 // PG entries
-const std::string SAM_PG_BEGIN_TOKEN     = "@PG";
-const std::string SAM_PG_NAME_TAG        = "ID";
-const std::string SAM_PG_VERSION_TAG     = "VN";
-const std::string SAM_PG_COMMANDLINE_TAG = "CL";
+const std::string SAM_PG_BEGIN_TOKEN         = "@PG";
+const std::string SAM_PG_COMMANDLINE_TAG     = "CL";
+const std::string SAM_PG_ID_TAG              = "ID";
+const std::string SAM_PG_NAME_TAG            = "PN";
+const std::string SAM_PG_PREVIOUSPROGRAM_TAG = "PP";
+const std::string SAM_PG_VERSION_TAG         = "VN";
 
 // CO entries
 const std::string SAM_CO_BEGIN_TOKEN = "@CO";
@@ -63,6 +70,7 @@ const std::string SAM_CO_BEGIN_TOKEN = "@CO";
 // HD:SO values
 const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate";
 const std::string SAM_HD_SORTORDER_QUERYNAME  = "queryname";
+const std::string SAM_HD_SORTORDER_UNKNOWN    = "unknown";
 const std::string SAM_HD_SORTORDER_UNSORTED   = "unsorted";
 
 // HD:GO values
@@ -74,29 +82,14 @@ const std::string SAM_HD_GROUPORDER_REFERENCE = "reference";
 const unsigned int SAM_SQ_LENGTH_MIN = 1;
 const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
 
-// --------------
 // RG:PL values
-
-// 454
-const std::string SAM_RG_SEQTECHNOLOGY_454         = "454";
-const std::string SAM_RG_SEQTECHNOLOGY_LS454_LOWER = "ls454";
-const std::string SAM_RG_SEQTECHNOLOGY_LS454_UPPER = "LS454";
-
-// Helicos
-const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_LOWER = "helicos";
-const std::string SAM_RG_SEQTECHNOLOGY_HELICOS_UPPER = "HELICOS";
-
-// Illumina
-const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_LOWER = "illumina";
-const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA_UPPER = "ILLUMINA";
-
-// PacBio
-const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_LOWER = "pacbio";
-const std::string SAM_RG_SEQTECHNOLOGY_PACBIO_UPPER = "PACBIO";
-
-// SOLiD
-const std::string SAM_RG_SEQTECHNOLOGY_SOLID_LOWER = "solid";
-const std::string SAM_RG_SEQTECHNOLOGY_SOLID_UPPER = "SOLID";
+const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY  = "CAPILLARY";
+const std::string SAM_RG_SEQTECHNOLOGY_HELICOS    = "HELICOS";
+const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA   = "ILLUMINA";
+const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT";
+const std::string SAM_RG_SEQTECHNOLOGY_LS454      = "LS454";
+const std::string SAM_RG_SEQTECHNOLOGY_PACBIO     = "PACBIO";
+const std::string SAM_RG_SEQTECHNOLOGY_SOLID      = "SOLID";
 
 } // namespace Constants
 } // namespace BamTools