[med-svn] [Git][med-team/mafft][master] 3 commits: New upstream version 7.407

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / mafft


Commits:
f5b755f2 by Steffen Moeller at 2018-11-28T11:45:04Z
New upstream version 7.407
- - - - -
5f66708d by Steffen Moeller at 2018-11-28T11:45:07Z
Update upstream source from tag 'upstream/7.407'

Update to upstream version '7.407'
with Debian dir 43d38b55291d2de6f9af25730ef464d703409bcb
- - - - -
31d2e64a by Steffen Moeller at 2018-11-28T11:50:28Z
Preparing for 7.407

- - - - -


7 changed files:

- core/dvtditr.c
- core/mafft.bat
- core/mafft.tmpl
- core/mltaln.h
- debian/changelog
- debian/control
- readme


Changes:

=====================================
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
=====================================
@@ -1,5 +1,13 @@
 @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
=====================================
@@ -1,7 +1,7 @@
 #! /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
=====================================
@@ -1,3 +1,13 @@
+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 at 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 at 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
=====================================
@@ -1,6 +1,6 @@
 -----------------------------------------------------------------------
   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 at ifrec.osaka-u.ac.jp



View it on GitLab: https://salsa.debian.org/med-team/mafft/compare/8c005a413a742080801d774e08134e817f2aba53...31d2e64a240a431bb4cf6865cce9c2be3aba62ae

-- 
View it on GitLab: https://salsa.debian.org/med-team/mafft/compare/8c005a413a742080801d774e08134e817f2aba53...31d2e64a240a431bb4cf6865cce9c2be3aba62ae
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181128/1cd5c9ae/attachment-0001.html>