core/dvtditr.c

@@ -481,6 +481,8 @@ int main( int argc, char *argv[] )
 
 	nkozo = 0;
 
+
+
 	if( njob < 2 ) 
 	{
 		seq = AllocateCharMtx( 2, nlenmax*1+1 );
@@ -501,6 +503,25 @@ int main( int argc, char *argv[] )
 	}
 
 
+	if( nlenmax < 1 )
+	{
+		seq = AllocateCharMtx( njob, nlenmax*1+1 );
+    	name = AllocateCharMtx( njob, B+1 );
+//	    nlen = AllocateIntVec( 2 ); 
+		readData_pointer( infp, name, nlen, seq );
+		fclose( infp );
+		initFiles();
+		for( i=0; i<njob; i++ ) strcpy( seq[i], "" );
+		writeData_pointer( prep_g, njob, name, nlen, seq );
+		reporterr( "Warning: No sequence found.\n", njob ); 
+		FreeCharMtx( seq );
+		FreeCharMtx( name );
+//		free( nlen );
+		closeFiles();
+		exit( 0 );
+	}
+
+
 	if( subalignment )
 	{
 		readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );

core/mafft.bat

 @echo off
 setlocal enabledelayedexpansion
+cls
+for /f "usebackq tokens=*" %%i IN (`cd`) DO @set current_dir=%%i
+if /i "%current_dir%" == "%windir%" (
+  set mafft_working_dir="%~dp0"
+) else (
+  set mafft_working_dir="%current_dir%"
+)
+pushd "%mafft_working_dir%"
 
 echo; 1>&2
 echo Preparing environment to run MAFFT on Windows. 1>&2
@@ -21,4 +29,5 @@ REM temporary folder.
 
 "%ROOTDIR%\usr\bin\bash" "%ROOTDIRWBS%\usr\bin\mafft" %*
 
+popd
 exit /b

core/mafft.tmpl

 #! /bin/bash 
 er=0;
 myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.402 (2018/May/23)"; export version
+version="v7.407 (2018/Jul/23)"; export version
 LANG=C; export LANG
 os=`uname`
 progname=`basename "$0"`
@@ -2625,6 +2625,8 @@ BEGIN {
 	prefix = ENVIRON["prefix"];
 	version = ENVIRON["version"];
 	myself = ENVIRON["myself"];
+	pwd = ENVIRON["mafft_working_dir"];  # from mafft.bat on windows
+	if( pwd == "" ) pwd = ENVIRON["PWD"];
 	while( 1 )
 	{
 		options = ""
@@ -2642,7 +2644,7 @@ BEGIN {
 		while( 1 )
 		{
 			printf( "\n" ) > "/dev/tty";
-			printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
+			printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty";
 			res = getline < "/dev/tty";
 			close( "/dev/tty" )
 			if( res == 0 || NF == 0 )

core/mltaln.h

@@ -35,7 +35,7 @@
 
 
 
-#define VERSION "7.402"
+#define VERSION "7.407"
 #define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )
 
 #define FFT_THRESHOLD  80

debian/changelog

+mafft (7.407-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream version.
+    7.380–7.392 had a bug in the --add and --merge options
+  * Standards-Version: 4.2.1
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 28 Nov 2018 12:46:29 +0100
+
 mafft (7.402-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/mafft
 Vcs-Git: https://salsa.debian.org/med-team/mafft.git
 Homepage: http://mafft.cbrc.jp/alignment/software/

readme

 -----------------------------------------------------------------------
   MAFFT: a multiple sequence alignment program
-  version 7.402, 2018/May/23
+  version 7.407, 2018/Jul/23
 
   http://mafft.cbrc.jp/alignment/software/
   katoh@ifrec.osaka-u.ac.jp