Bug fix release 4.2.5

Addresses issue #174

Author: evolarjun

.github/workflows/binary.yml

@@ -11,6 +11,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
         - uses: actions/checkout@v4
         - name: prerequisites

.github/workflows/ccpp.yml

@@ -9,6 +9,7 @@ on:
 jobs:
   linux_x86:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - name: prerequisites
@@ -35,6 +36,7 @@ jobs:
           path: amrfinder_binaries_v*.tar.gz
   linux-arm64:
     runs-on: ubuntu-24.04-arm
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - name: prerequisites

.github/workflows/conda.yml

@@ -9,6 +9,7 @@ on:
 jobs:
   conda_linux_x86_64:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
     - name: When was this run
       run: date
@@ -51,6 +52,7 @@ jobs:
           bash ./test_amrfinder.sh -p
   conda_linux_aarch64:
     runs-on: ubuntu-24.04-arm
+    timeout-minutes: 30
     steps:
     - uses: conda-incubator/setup-miniconda@v3
       with:

.github/workflows/dockerhub.yml

@@ -10,9 +10,8 @@ on:
 jobs:
 
   test_dockerhub:
-
     runs-on: ubuntu-latest
-
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - name: Test docker

.github/workflows/mac_ccpp.yml

@@ -9,6 +9,7 @@ on:
 jobs:
   macos_arm:
     runs-on: macos-latest
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - name: submodule checkout
@@ -41,6 +42,7 @@ jobs:
           path: amrfinder_binaries_macos_aarch64_v*.tar.gz
   macos_x86_64:
     runs-on: macos-13
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4
     - name: submodule checkout

.github/workflows/mac_conda.yml

@@ -8,6 +8,7 @@ on:
 jobs:
   conda_macos_aarch64:
     runs-on: macos-latest
+    timeout-minutes: 30
     steps:
     - name: Install conda because built-in conda is borked
       run: |
@@ -57,6 +58,7 @@ jobs:
           bash ./test_amrfinder.sh -p 
   conda_macos_x86_64:
     runs-on: macos-13
+    timeout-minutes: 30
     steps:
     - name: Install conda because built-in conda is borked
       run: |

amrfinder.cpp

@@ -33,6 +33,7 @@
 * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional)
 *
 * Release changes:
+*   4.2.5   12/05/2025 PD-5507  add AMRProt-susceptible.fa to amrfinder_update.cpp
 *   4.2.4   12/02/2025 PD-5495  If set use CURL_CA_BUNDLE environment variable for certificate authorities
 *   4.2.3   10/16/2025 PD-5469  QC_ASSERT error messages of amrfinder_update.cpp are made human readable
 *   4.2.2   09/25/2025 PD-5395  cirA_A169AERSPHNFPKATer becomes cirA_A169insTer10, ompK35_N...Y82del becomes ompK35_N82_Y310del

amrfinder_update.cpp

@@ -38,8 +38,8 @@
 
 
 // PAR
+#undef TEST_UPDATE  
 #define HTTPS 1   // 0: FTP
-//#define TEST_UPDATE  
 
 
 
@@ -58,13 +58,15 @@ namespace
 {
 
 
+// URL
 #ifdef TEST_UPDATE
   #define URL "https://ftp.ncbi.nlm.nih.gov/pathogen/Technical/AMRFinder_technical/test_database/"
 #else
+  #define URL_SUF "://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/"  
   #if HTTPS
-    #define URL "https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/"  
+    #define URL  "https" URL_SUF
   #else
-    #define URL "ftp://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/"  
+    #define URL  "ftp" URL_SUF
   #endif
 #endif
 
@@ -343,6 +345,7 @@ Requirement: the database directory contains subdirectories named by database ve
     fetchAMRFile (curl, urlDir, latestDir, "AMRProt.fa");
     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-mutation.tsv");
     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-suppress.tsv");
+    fetchAMRFile (curl, urlDir, latestDir, "AMRProt-susceptible.fa");
     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-susceptible.tsv");
     fetchAMRFile (curl, urlDir, latestDir, "AMR_CDS.fa");
     fetchAMRFile (curl, urlDir, latestDir, "database_format_version.txt");  // PD-3051 

common.hpp

@@ -206,7 +206,7 @@ template <typename T /*:number*/>
   inline bool between (T x, T low, T high)
     { return x >= low && x < high; }
 
-template <typename T/*:number*/> 
+template <typename T /*:number*/> 
   inline bool betweenEqual (T x, T low, T high)
     { return x >= low && x <= high; }
 
@@ -2536,6 +2536,19 @@ template <typename T>
             toDelete--;
           }
         }
+    Vector<T> subvec (size_t from,
+                      size_t count = no_index) const
+      { Vector<T> res;  
+        if (from >= P::size ())
+          return res;
+        size_t size = P::size () - from;
+        if (count != no_index)
+          minimize (size, count);
+        res. reserve (size);
+        for (size_t i = 0; i < size; i++)
+          res << (*this) [from + i];
+        return res;
+      }
 
     void sort ()
       { if (ascending == etrue)
@@ -2686,8 +2699,7 @@ template <typename T>
         }
     template <typename U /* : T */>
       void setMinus (const Vector<U> &other)
-        { filterIndex ([&] (size_t i) { return other. containsFast ((*this) [i]); }); }
-        
+        { filterIndex ([&] (size_t i) { return other. containsFast ((*this) [i]); }); }        
     size_t findDuplicate (bool checkSortedP = true) const
       { if (P::size () <= 1)
           return no_index;
@@ -3079,6 +3091,10 @@ template <typename T /* : Root */>
 
 
 
+enum SetOperation {soIntersect, soUnion, soMinus};
+
+
+
 template <typename T>
   struct Set : set<T>
   {

curl_easy.hpp

@@ -67,19 +67,13 @@ struct Curl
 
   Curl ()
     : eh (curl_easy_init ())
-    { 
-        if (! eh)
-            throw runtime_error ("Cannot initialize curl_easy");
-
-        // Check environment variable CURL_CA_BUNDLE for CA path
-        // PD-5495 / https://github.com/ncbi/amr/issues/170
-        const char *env_ca_bundle = getenv("CURL_CA_BUNDLE");
-        if (env_ca_bundle) {
-            // Override the libcurl system-wide default
-            curl_easy_setopt(eh, CURLOPT_CAINFO, env_ca_bundle);
-        }
+    { if (! eh)
+        throw runtime_error ("Cannot initialize curl_easy");        
+      // Override the libcurl system-wide default
+      // PD-5495 / https://github.com/ncbi/amr/issues/170
+      if (const char *env_ca_bundle = getenv ("CURL_CA_BUNDLE"))          
+        curl_easy_setopt (eh, CURLOPT_CAINFO, env_ca_bundle);  
     }
-
  ~Curl ()
    { curl_easy_cleanup (eh); }