PD-4888 mutate.cpp is added

evolarjun · Feb 27, 2024 · d2d9846 · d2d9846
1 parent 9405804
commit d2d9846
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Showing 6 changed files with 21 additions and 12 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,12 +2,13 @@ data/
 *.o
 amr_report
 amrfinder
-fasta_check
-fasta_extract
-dna_mutation
-gff_check
 amrfinder_index
 amrfinder_update
 amrfinder_customize
+dna_mutation
+fasta_check
+fasta_extract
 fasta2parts
+gff_check
+mutate
 *.got
diff --git a/Makefile b/Makefile
@@ -83,7 +83,7 @@ COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c
 
 .PHONY: all clean install release 
 
-BINARIES= amr_report amrfinder amrfinder_index amrfinder_update fasta_check fasta_extract fasta2parts gff_check dna_mutation 
+BINARIES= amr_report amrfinder amrfinder_index amrfinder_update fasta_check fasta_extract fasta2parts gff_check dna_mutation mutate
 
 all:	$(BINARIES)
 
@@ -95,6 +95,7 @@ common.o:	common.hpp common.inc
 curl_easy.o: curl_easy.hpp common.hpp common.inc
 gff.o: gff.hpp common.hpp common.inc
 alignment.o:	alignment.hpp alignment.hpp common.inc
+seq.o: seq.hpp common.hpp common.inc
 
 amr_report.o:	common.hpp common.inc gff.hpp alignment.hpp
 amr_reportOBJS=amr_report.o common.o gff.o alignment.o
@@ -145,6 +146,11 @@ dna_mutationOBJS=dna_mutation.o common.o alignment.o
 dna_mutation:	$(dna_mutationOBJS)
 	$(CXX) -o $@ $(dna_mutationOBJS)
 
+mutate.o:	common.hpp common.inc alignment.hpp seq.hpp
+mutateOBJS=mutate.o common.o alignment.o seq.o
+mutate:	$(mutateOBJS)
+	$(CXX) -o $@ $(mutateOBJS)
+
 
 
 clean:

diff --git a/amrfinder.cpp b/amrfinder.cpp
@@ -33,6 +33,7 @@
 * Dependencies: NCBI BLAST, HMMer, gunzip (optional)
 *
 * Release changes:
+*   3.12.13 02/27/2024 PD-4888  mutation.cpp is added to the distribution (used only in testing)
 *   3.12.12 02/21/2024 PD-4906  --print_node for fusion proteins
 *                               move DOCUMENTATION section to the end of the usage message
 *   3.12.11 02/13/2024 PD-4893  move DOCUMENTATION and UPDATES sections to the end of the --help message

diff --git a/common.cpp b/common.cpp
@@ -265,15 +265,16 @@ namespace
     cxml->print (string (error_caption) + ": " + msg);
 
   if (segmFault)
-    abort ();
+    abort ();    
   exit (1);
 }
 
 
 
-[[noreturn]] void errorExitStr (const string &msg)
+void errorExitStr (const string &msg)
 { 
-  errorExit (msg. c_str ()); 
+  if (! uncaught_exceptions ())
+    errorExit (msg. c_str ()); 
 }
 
 

diff --git a/common.hpp b/common.hpp
@@ -147,11 +147,11 @@ constexpr const char* error_caption ("*** ERROR ***");
 	// Update: *logPtr
 	// Invokes: if segmFault then abort() else exit(1)
 
-[[noreturn]] void errorExitStr (const string &msg);
-  // For debugger
+void errorExitStr (const string &msg);
+  // For debugger: should not be inline
 
 [[noreturn]] void throwf (const string &s); 
-  // For debugger: should not be in-line
+  // For debugger: should not be inline
 
 void beep ();
   // Requires: !isRedirected()

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-3.12.12
+3.12.13