Merge branch 'main' of https://github.com/rcedgar/muscle into main

.github/workflows/build_linux.yml

@@ -21,7 +21,7 @@ jobs:
           cd $GITHUB_WORKSPACE
           ls -lh
           cd src
-          make
+          make LDFLAGS2=-static
       - name: Upload binary artifact
         uses: actions/upload-artifact@v2
         with:

src/Makefile

@@ -26,10 +26,7 @@ endif
 
 CXXFLAGS := $(CXXFLAGS) -O3 -fopenmp -ffast-math
 
-LDFLAGS := $(LDFLAGS) -O3 -fopenmp -pthread -lpthread
-ifeq ($(OS),Linux)
-    LDFLAGS += -static
-endif
+LDFLAGS := $(LDFLAGS) -O3 -fopenmp -pthread -lpthread ${LDFLAGS2}
 
 HDRS := $(shell echo *.h)
 OBJS := $(shell echo *.cpp | sed "-es/^/$(OS)\//" | sed "-es/ / $(OS)\//g" | sed "-es/\.cpp/.o/g")

src/countsort.h

@@ -20,7 +20,7 @@ class CountSortMem
 	CountSortMem()
 		{
 		m_MaxValueCount = 0;
-		zero(m_Vecs, NVEC);
+		memset_zero(m_Vecs, NVEC);
 		}
 
 	void Free()

src/ensemble.cpp

@@ -41,7 +41,7 @@ void Ensemble::SortMSA(MSA &M)
 	M.GetLabelToSeqIndex(Labels2, LabelToSeqIndex2);
 
 	char **szSeqsSorted = myalloc(char *, SeqCount);
-	zero(szSeqsSorted, SeqCount);
+	memset_zero(szSeqsSorted, SeqCount);
 	for (uint SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex)
 		{
 		const string &Label = Labels2[SeqIndex];

src/gitver.bash

@@ -1,5 +1,13 @@
 #!/bin/bash
 
+if [ ! -d ../.git ] ; then
+  if [ ! -f gitver.txt ] ; then
+    echo "0" > gitver.txt
+  fi
+  echo "Repo not found, git hash set to zero"
+  exit 0
+fi
+
 PATH=$PATH:/usr/bin
 
 git describe --abbrev=6 --dirty --long --always \

src/gitver.bat

@@ -3,7 +3,7 @@
 if exist gitver.txt (
 	echo gitver.txt found
 ) else (
-	echo 000 > gitver.txt
+	echo "-" > gitver.txt
 )
 
 if exist c:\cygwin64\bin\bash.exe (

src/help.h

@@ -49,7 +49,7 @@
 "\n"
 "Update ensemble by adding two sequences of digits to each replicate, digits\n"
 "are column confidence (CC) values, e.g. \"73\" means CC=0.73, \"++\" is CC=1.0:\n"
-"    muscle -addconfseqs ensemble.efa -output ensemble_cc.efa\n"
+"    muscle -addconfseq ensemble.efa -output ensemble_cc.efa\n"
 "\n"
 "Calculate letter confidence (LC) values, -ref specifies the alignment to\n"
 "compare against the ensemble (e.g. from -maxcc), output is in aligned\n"

src/help.txt

@@ -49,7 +49,7 @@ Convert FASTA to EFA, input has one filename per line:
 
 Update ensemble by adding two sequences of digits to each replicate, digits
 are column confidence (CC) values, e.g. "73" means CC=0.73, "++" is CC=1.0:
-    muscle -addconfseqs ensemble.efa -output ensemble_cc.efa
+    muscle -addconfseq ensemble.efa -output ensemble_cc.efa
 
 Calculate letter confidence (LC) values, -ref specifies the alignment to
 compare against the ensemble (e.g. from -maxcc), output is in aligned

src/myutils.cpp

@@ -807,7 +807,7 @@ static char *GetThreadStr()
 		{
 		unsigned NewThreadStrCount = ThreadIndex + 4;
 		char **NewThreadStrs = myalloc(char *, NewThreadStrCount);
-		zero(NewThreadStrs, NewThreadStrCount);
+		memset_zero(NewThreadStrs, NewThreadStrCount);
 		if (g_ThreadStrCount > 0)
 			memcpy(NewThreadStrs, g_ThreadStrs, g_ThreadStrCount*sizeof(char *));
 		g_ThreadStrs = NewThreadStrs;
@@ -898,6 +898,8 @@ void Log(const char *Format, ...)
 
 void Die_(const char *Format, ...)
 	{
+	va_list ArgList;
+	va_start(ArgList, Format);
 #pragma omp critical
 	{
 	static bool InDie = false;
@@ -908,10 +910,7 @@ void Die_(const char *Format, ...)
 
 	if (g_fLog != 0)
 		setbuf(g_fLog, 0);
-	va_list ArgList;
-	va_start(ArgList, Format);
 	myvstrprintf(Msg, Format, ArgList);
-	va_end(ArgList);
 
 	fprintf(stderr, "\n\n");
 	Log("\n");
@@ -944,6 +943,7 @@ void Die_(const char *Format, ...)
 
 	exit(1);
 	}
+	va_end(ArgList);
 	}
 
 void Warning_(const char *Format, ...)
@@ -2076,7 +2076,8 @@ void GetVersionString(string &s)
 	"T"
 #endif
 	;
-
+	if (GIT_VER == 0)
+		GIT_VER = "-";
 	Ps(s, "%s %s.%s%s [%s]", PROGRAM_NAME, MY_VERSION, GetPlatform(), Flags, GIT_VER);
 	}
 

src/myutils.h

@@ -358,7 +358,6 @@ inline bool feq(double x, double y)
 #define asserteq(x, y)	assert(feq(x, y))
 #define assertaeq(x, y)	asserta(feq(x, y))
 
-#define	zero(a, n)	memset((a), 0, (n)*sizeof(a[0]))
 #define	memset_zero(a, n)	memset((a), 0, (n)*sizeof(a[0]))
 
 void ResetRand(unsigned Seed);