PD-4923 Verify the version of StxTyper when AMRFinderPlus is run

amrfinder.cpp

@@ -33,6 +33,7 @@
 * Dependencies: NCBI BLAST, HMMer, gunzip (optional)
 *
 * Release changes:
+* 3.12.16 03/08/2024 PD-4923 verify the version of stxtyper
 * 3.12.15 03/05/2024 PD-4918 stxtyper ver. 1.0.14: --print_node 
 * stxtyper -q
 * 3.12.14 03/05/2024 PD-4910 -n <nucl> --plus -O Escherichia: stxtyper 1.0.13 is invoked, STX* classes are suppressed in amr_report.cpp
@@ -849,6 +850,20 @@ struct ThisApplication : ShellApplication
 
 
  const bool blastn = ! emptyArg (dna) && ! organism1. empty () && fileExists (db + "/AMR_DNA-" + organism1);
+ const bool stxTyper = blastn && organism1 == "Escherichia" && add_plus;
+
+
+ if (stxTyper)
+ {
+ const string verFName (tmp + "/stxtyper-ver");
+ exec (fullProg ("stxtyper") + " -v > " + verFName, logFName);
+ LineInput f (verFName);
+ if (! f. nextLine ())
+ throw runtime_error ("Cannot get the version of StxTyper");
+ const string stxTyperVersion ("1.0.14"); // PAR
+ if (f. line != stxTyperVersion)
+ throw runtime_error ("AMRFinder invokes StxTyper version " + f. line + ". Expected StxTyper version is " + stxTyperVersion); 
+ }
 
 
  // Create files for amr_report 
@@ -1118,7 +1133,6 @@ struct ThisApplication : ShellApplication
  }
 
 
- const bool stxTyper = blastn && organism1 == "Escherichia" && add_plus;
  if (stxTyper)
  {
  stderr. section ("Running stxtyper");

common.hpp

@@ -2355,6 +2355,17 @@ template <typename T>
  { if (P::empty ())
  return no_index;
  checkSorted ();
+ if (P::size () < 8) // PAR
+ {
+ for (size_t i = 0; i < P::size (); i++)
+ {
+ if (value == (*this) [i])
+ return i;
+ if (value < (*this) [i])
+ return exact ? no_index : i;
+ }
+ return no_index;
+ }
  size_t lo = 0; // vec.at(lo) <= value
  size_t hi = P::size () - 1; 
  // lo <= hi

version.txt

@@ -1 +1 @@
-3.12.15
+3.12.16