PD-5085: Change column "Element length" to "Target length"; StxTyper …

…ver. 1.0.26; "::" is a fusion infix for hierarchy_node
ncbi · Oct 22, 2024 · 7375d92 · 7375d92
1 parent 31cf165
commit 7375d92
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Showing 5 changed files with 14 additions and 6 deletions.
diff --git a/amr_report.cpp b/amr_report.cpp
@@ -838,15 +838,15 @@ struct BlastAlignment : Alignment
         return getGeneSymbol ();
       string s;
       for (const BlastAlignment* fusion : fusions)
-        add (s, "/", fusion->getGeneSymbol ());
+        add (s, "/" /*fusion_infix*/, fusion->getGeneSymbol ());  // PD-5155 ??
       return s;
     }
   string fusion2famIds () const
     { if (isMutationProt () || fusions. empty ())
         return famId;
       string s;
       for (const BlastAlignment* fusion : fusions)
-        add (s, "/", fusion->famId);
+        add (s, fusion_infix, fusion->famId);
       return s;
     }
 private:

diff --git a/amrfinder.cpp b/amrfinder.cpp
@@ -33,6 +33,9 @@
 * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional)
 *
 * Release changes:
+*   4.0.1   10/22/2024 PD-5155  "::" as a fusion infix for hierarchy_node
+*                      PD-5085  Change column "Element length" to "Target length"
+*                      PD-5085  StxTyper version 1.0.26
 *   4.0.0   10/22/2024 PD-5156  StxTyper etc.
 *   3.13.3  09/11/2024          Instruction for -gff: "Locations are in the --nucleotide file."
 *                               StxTyper version 1.0.25
@@ -330,7 +333,7 @@ using namespace GFF_sp;
 const string dataVer_min ("2024-08-14.2");
   // 3.12: "2023-12-15.2"
   // 3.11: "2021-02-18.1"  
-const string stxTyperVersion ("1.0.25");  
+const string stxTyperVersion ("1.0.26");  
 
 
 

diff --git a/columns.hpp b/columns.hpp
@@ -52,7 +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";
@@ -62,3 +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: "/"
+
diff --git a/stxtyper b/stxtyper
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-4.0.0
+4.0.1
+41 −2		amrfinder_columns.hpp
+137 −46		common.cpp
+248 −134		common.hpp
+1 −1		common.inc
+2 −1		stxtyper.cpp
+1 −1		test/amrfinder_integration.expected
+1 −1		test/amrfinder_integration2.expected
+1 −0		tsv.hpp
+1 −1		version.txt