From 09d052a9fae6df7c335ecd692d23277c1abe9aa6 Mon Sep 17 00:00:00 2001
From: Vyacheslav Brover <vyacheslav.brover@nih.gov>
Date: Fri, 20 Dec 2024 15:10:59 -0500
Subject: [PATCH] PD-5201 Change empty fields to NA

---
 amr_report.cpp   | 3 +--
 amrfinder.cpp    | 3 ++-
 columns.hpp      | 3 ++-
 dna_mutation.cpp | 2 +-
 stx              | 2 +-
 version.txt      | 2 +-
 6 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/amr_report.cpp b/amr_report.cpp
index 8f622b5..1f44223 100644
--- a/amr_report.cpp
+++ b/amr_report.cpp
@@ -58,7 +58,6 @@ namespace
 constexpr bool useCrossOrigin = false;  // GPipe: true
 constexpr double frac_delta = 1e-5;  
 constexpr size_t domain_min = 20;  // aa
-const string na ("NA");
   
 bool ident_min_user = false;
 bool equidistant = false;
@@ -656,7 +655,7 @@ struct BlastAlignment final : Alignment
       	      td << input_name;;
             td << (targetProt ? nvl(targetName, na) : na);  // PD-2534
   	        if (cdsExist)
-  	          td << (empty () ? na : (cds. contig. empty () ? nvl (targetName,na)  : cds. contig))
+  	          td << (empty () ? na : (cds. contig. empty () ? nvl (targetName, na)  : cds. contig))
   	             << (empty () ? 0  : (cds. contig. empty () ? targetStart : cds. start) + 1)
   	             << (empty () ? 0  : (cds. contig. empty () ? targetEnd  : cds. stop))
   	             << (empty () ? na : (cds. contig. empty () ? (targetStrand ? "+" : "-") : (cds. strand ? "+" : "-")));
diff --git a/amrfinder.cpp b/amrfinder.cpp
index c6ca7f5..eada1ee 100644
--- a/amrfinder.cpp
+++ b/amrfinder.cpp
@@ -33,6 +33,7 @@
 * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional)
 *
 * Release changes:
+*   4.0.9   12/20/2024 PD-5201  SrxTyper ver. 1.0.32
 *   4.0.8   12/18/2024 PD-5181  StxTyper ver. 1.0.31
 *           12/14/2024 PD-5191  stxtyper --threads
 *   4.0.7   12/12/2024 PD-5192  StxTyper ver. 1.0.30
@@ -342,7 +343,7 @@ 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 ("1.0.31");  
+const string stxTyperVersion ("1.0.32");  
 
 
 
diff --git a/columns.hpp b/columns.hpp
index cf25a92..4d5b1a3 100644
--- a/columns.hpp
+++ b/columns.hpp
@@ -66,4 +66,5 @@ constexpr const char* hierarchyNode_colName = "Hierarchy node";
 
 // PD-5155
 constexpr const char* fusion_infix = "::";  // was: "/"
-  
\ No newline at end of file
+  
+constexpr const char* na ("NA");
diff --git a/dna_mutation.cpp b/dna_mutation.cpp
index 803ec9f..2e2c031 100644
--- a/dna_mutation.cpp
+++ b/dna_mutation.cpp
@@ -108,7 +108,7 @@ struct BlastnAlignment final : Alignment
     }
   void report (TsvOut& td,
                bool mutationAll) const 
-    { const string na ("NA");
+    { //const string na ("NA");
       for (const SeqChange& seqChange : seqChanges)
       {
         VectorPtr<AmrMutation> mutations (seqChange. mutations);
diff --git a/stx b/stx
index 24ec79d..a9b7b05 160000
--- a/stx
+++ b/stx
@@ -1 +1 @@
-Subproject commit 24ec79d025481df37f47635b976380a71818d0f4
+Subproject commit a9b7b05298aa04c9624cc814c6c293bd710e8ce6
diff --git a/version.txt b/version.txt
index a2cec7a..7919852 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-4.0.8
+4.0.9