Merge pull request #7 from ncbi/dev

Merge release to include changes for running with AMRFinderPlus 4.0
ncbi · Oct 26, 2024 · 3dede55 · 3dede55
2 parents ba33f57 + de398b2
commit 3dede55
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Showing 9 changed files with 441 additions and 194 deletions.
diff --git a/amrfinder_columns.hpp b/amrfinder_columns.hpp
@@ -1,4 +1,38 @@
-// AMRFinderPlus column names
+// columns.hpp
+
+/*===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE                          
+*               National Center for Biotechnology Information
+*                                                                          
+*  This software/database is a "United States Government Work" under the   
+*  terms of the United States Copyright Act.  It was written as part of    
+*  the author's official duties as a United States Government employee and 
+*  thus cannot be copyrighted.  This software/database is freely available 
+*  to the public for use. The National Library of Medicine and the U.S.    
+*  Government have not placed any restriction on its use or reproduction.  
+*                                                                          
+*  Although all reasonable efforts have been taken to ensure the accuracy  
+*  and reliability of the software and data, the NLM and the U.S.          
+*  Government do not and cannot warrant the performance or results that    
+*  may be obtained by using this software or data. The NLM and the U.S.    
+*  Government disclaim all warranties, express or implied, including       
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.                                                                
+*                                                                          
+*  Please cite the author in any work or product based on this material.   
+*
+* ===========================================================================
+*
+* Author: Vyacheslav Brover
+*
+* File Description:
+*   AMRFinderPlus column names
+*
+*/
+
+
+
 // PD-5085
 
 constexpr const char* prot_colName = "Protein id";   // PD-2534  
@@ -18,7 +52,7 @@ constexpr const char* class_colName = "Class";
 constexpr const char* subclass_colName = "Subclass";
 //        
 constexpr const char* method_colName = "Method";
-constexpr const char* targetLen_colName = "Element length";  // was: "Target length" ??
+constexpr const char* targetLen_colName = "Target length";  // was: "Element length" (temporarily)
 constexpr const char* refLen_colName = "Reference sequence length";
 constexpr const char* refCov_colName = "% Coverage of reference";
 constexpr const char* refIdent_colName = "% Identity to reference";
@@ -28,3 +62,8 @@ constexpr const char* closestRefName_colName = "Closest reference name";
 constexpr const char* hmmAccession_colName = "HMM accession";
 constexpr const char* hmmDescr_colName = "HMM description";
 constexpr const char* hierarchyNode_colName = "Hierarchy node";
+
+
+// PD-5155
+constexpr const char* fusion_infix = "::";  // was: "/"
+