[med-svn] [Git][med-team/mafft][master] 3 commits: New upstream version 7.481
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Jun 11 21:40:48 BST 2021
Nilesh Patra pushed to branch master at Debian Med / mafft
Commits:
82da29e9 by Nilesh Patra at 2021-06-12T02:06:38+05:30
New upstream version 7.481
- - - - -
0f69c3dc by Nilesh Patra at 2021-06-12T02:06:42+05:30
Update upstream source from tag 'upstream/7.481'
Update to upstream version '7.481'
with Debian dir d0ebb518c1828bacb8a40c53653b73aec6937f42
- - - - -
b23f7f46 by Nilesh Patra at 2021-06-12T02:07:06+05:30
Interim changelog entry
- - - - -
13 changed files:
- MPI/mltaln9_mpi.c
- core/blosum.c
- core/dash_client.go
- core/functions.h
- core/io.c
- core/mafft.tmpl
- core/mltaln.h
- core/mltaln9.c
- core/tbfast.c
- core/tditeration.c
- core/univscript.tmpl
- debian/changelog
- readme
Changes:
=====================================
MPI/mltaln9_mpi.c
=====================================
@@ -1,5 +1,6 @@
#include "mltaln.h"
#include <mpi.h>
+
#ifdef enableatomic
#include <stdatomic.h>
#endif
@@ -12982,7 +12983,7 @@ void dontcalcimportance_firstone( int nseq, double *eff, char **seq, LocalHom **
#endif
}
-void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr )
+void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr, int alloclen )
{
int i, j, pos, len, ti, tj;
double *importance; // static -> local, 2012/02/25
@@ -12991,7 +12992,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
int *nogaplen; // static -> local, 2012/02/25
LocalHom *tmpptr;
- importance = AllocateDoubleVec( nlenmax );
+ importance = AllocateDoubleVec( alloclen );
nogaplen = AllocateIntVec( nseq );
ieff = AllocateDoubleVec( nseq );
@@ -13025,7 +13026,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
{
i = targetmapr[ti];
// reporterr( "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
importance[pos] = 0.0;
for( j=0; j<nseq; j++ )
{
@@ -13048,7 +13049,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
}
#if 0
reporterr( "position specific importance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
reporterr( "%d: %f\n", pos, importance[pos] );
reporterr( "\n" );
#endif
@@ -13215,7 +13216,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
free( ieff );
}
-void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom )
+void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom, int alloclen )
{
int i, j, pos, len;
double *importance; // static -> local, 2012/02/25
@@ -13224,7 +13225,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
int *nogaplen; // static -> local, 2012/02/25
LocalHom *tmpptr;
- importance = AllocateDoubleVec( nlenmax );
+ importance = AllocateDoubleVec( alloclen );
nogaplen = AllocateIntVec( nseq );
ieff = AllocateDoubleVec( nseq );
@@ -13256,7 +13257,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
for( i=0; i<nseq; i++ )
{
// reporterr( "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
importance[pos] = 0.0;
for( j=0; j<nseq; j++ )
{
@@ -13299,7 +13300,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
}
#if 0
reporterr( "position specific importance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
reporterr( "%d: %f\n", pos, importance[pos] );
reporterr( "\n" );
#endif
=====================================
core/blosum.c
=====================================
@@ -397,6 +397,7 @@ static void overridematrix( double **matrix )
matrix[i1][i2] = v;
matrix[i2][i1] = v; // 2018/May/11
}
+ fclose( fp );
}
void extendedmtx( double **matrix, double *freq, unsigned char *amino, char *amino_grp )
=====================================
core/dash_client.go
=====================================
@@ -20,7 +20,7 @@ var VersionNumber = 1.1
var Debug = false
var NumberOfQueryTries = 12
var HTTPClient = &http.Client{}
-var SequenceLimit = 750
+var SequenceLimit = 3000
var AlignmentLimit = 10000
//URL's
=====================================
core/functions.h
=====================================
@@ -62,12 +62,12 @@ extern int searchAnchors( int nseq, char **seq, Segment *seg );
extern char *progName( char *str );
extern void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void dontcalcimportance_target( int nseq, double *eff, char **seq, LocalHom **localhom, int ntarget );
-extern void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr );
+extern void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr, int alloclen );
extern void dontcalcimportance_lastone( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void dontcalcimportance_firstone( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void dontcalcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
-extern void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom );
+extern void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom, int alloclen );
extern void weightimportance2( int nseq, double *eff, LocalHom **localhom );
extern void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom );
extern void extendlocalhom( int nseq, LocalHom **localhom );
=====================================
core/io.c
=====================================
@@ -432,7 +432,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ if( tmppt->overlapaa>0)
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -489,7 +492,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ if( tmppt->overlapaa>0)
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -516,7 +522,10 @@ void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off
for( tmppt=subnosento; tmppt; tmppt=tmppt->next )
{
tmppt->overlapaa = sumoverlap;
- tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+ if( tmppt->overlapaa>0)
+ tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+ else
+ tmppt->opt = -1.0;
fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
}
}
@@ -568,7 +577,10 @@ void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ if( tmppt->overlapaa>0)
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -623,7 +635,10 @@ void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ if( tmppt->overlapaa>0)
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -755,7 +770,10 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ if(tmppt->overlapaa>0)
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -812,7 +830,10 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off
if( divpairscore )
{
tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ if(tmppt->overlapaa>0)
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ else
+ tmppt->opt = -1.0;
}
else
{
@@ -836,8 +857,11 @@ void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off
for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
{
tmppt->overlapaa = sumoverlap;
- tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
-// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+ if(tmppt->overlapaa>0)
+ tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
+ else
+ tmppt->opt = -1.0;
+// fprintf( stderr, "tmpptr->opt = %f, sumoverlap=%d\n", tmppt->opt, sumoverlap );
}
}
}
=====================================
core/mafft.tmpl
=====================================
@@ -1,7 +1,7 @@
#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.475 (2020/Nov/23)"; export version
+version="v7.481 (2021/May/26)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
@@ -1034,7 +1034,7 @@ if [ $# -gt 0 ]; then
TMPFILE=`cygpath -w "$TMPFILE"` # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
fi
- umask 077
+# umask 077 # 2021/Jan
# mkdir "$TMPFILE" || er=1
@@ -2373,7 +2373,7 @@ $ownlist"
dashres="$?"
if [ $dashres -ne "0" ]; then
echo "Error in DASH" 1>>"$progressfile"
- echo "To use this feature, compiled with" 1>>"$progressfile"
+ echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile"
exit 1;
fi
@@ -2945,8 +2945,8 @@ BEGIN {
while( 1 )
{
go = 0;
- printf( "OK?\n" ) > "/dev/tty";
- printf( "@ [Y] " ) > "/dev/tty";
+ printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
if( res == 0 )
=====================================
core/mltaln.h
=====================================
@@ -36,7 +36,7 @@
-#define VERSION "7.475"
+#define VERSION "7.481"
#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
=====================================
core/mltaln9.c
=====================================
@@ -11528,7 +11528,7 @@ void dontcalcimportance_firstone( int nseq, double *eff, char **seq, LocalHom **
#endif
}
-void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr )
+void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, LocalHom **localhom, int *targetmap, int *targetmapr, int alloclen )
{
int i, j, pos, len, ti, tj;
double *importance; // static -> local, 2012/02/25
@@ -11537,7 +11537,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
int *nogaplen; // static -> local, 2012/02/25
LocalHom *tmpptr;
- importance = AllocateDoubleVec( nlenmax );
+ importance = AllocateDoubleVec( alloclen );
nogaplen = AllocateIntVec( nseq );
ieff = AllocateDoubleVec( nseq );
@@ -11571,7 +11571,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
{
i = targetmapr[ti];
// reporterr( "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
importance[pos] = 0.0;
for( j=0; j<nseq; j++ )
{
@@ -11594,7 +11594,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
}
#if 0
reporterr( "position specific importance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
reporterr( "%d: %f\n", pos, importance[pos] );
reporterr( "\n" );
#endif
@@ -11761,7 +11761,7 @@ void calcimportance_target( int nseq, int ntarget, double *eff, char **seq, Loca
free( ieff );
}
-void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom )
+void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom, int alloclen )
{
int i, j, pos, len;
double *importance; // static -> local, 2012/02/25
@@ -11770,7 +11770,8 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
int *nogaplen; // static -> local, 2012/02/25
LocalHom *tmpptr;
- importance = AllocateDoubleVec( nlenmax );
+ importance = AllocateDoubleVec( alloclen );
+// reporterr("alloclen=%d, nlenmax=%d\n", alloclen, nlenmax );
nogaplen = AllocateIntVec( nseq );
ieff = AllocateDoubleVec( nseq );
@@ -11802,8 +11803,10 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
for( i=0; i<nseq; i++ )
{
// reporterr( "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
+ for( pos=0; pos<alloclen; pos++ )
+ {
importance[pos] = 0.0;
+ }
for( j=0; j<nseq; j++ )
{
if( i == j ) continue;
@@ -11812,6 +11815,7 @@ void calcimportance_half( int nseq, double *eff, char **seq, LocalHom **localhom
{
for( tmpptr = localhom[i]+j-i; tmpptr; tmpptr=tmpptr->next )
{
+// reporterr( "pos=%d, alloclen=%d\n", pos, alloclen );
if( tmpptr->opt == -1 ) continue;
for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
{
=====================================
core/tbfast.c
=====================================
@@ -1337,10 +1337,10 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq
if( constraint && compacttree != 3 )
{
if( specifictarget )
- calcimportance_target( njob, ntarget, effarr, aseq, localhomtable, targetmap, targetmapr );
+ calcimportance_target( njob, ntarget, effarr, aseq, localhomtable, targetmap, targetmapr, *alloclen );
// dontcalcimportance_target( njob, effarr, aseq, localhomtable, ntarget ); //CHUUI
else
- calcimportance_half( njob, effarr, aseq, localhomtable );
+ calcimportance_half( njob, effarr, aseq, localhomtable, *alloclen );
// dontcalcimportance_half( njob, effarr, aseq, localhomtable ); //CHUUI
}
else if( constraint && nseed ) // ie, compacttree == 3 && constraint > 0
@@ -3320,10 +3320,10 @@ int main( int argc, char *argv[] )
if( constraint && compacttree != 3 )
{
if( specifictarget )
- calcimportance_target( njob, ntarget, eff, bseq, localhomtable, targetmap, targetmapr );
+ calcimportance_target( njob, ntarget, eff, bseq, localhomtable, targetmap, targetmapr, alloclen );
// dontcalcimportance_target( njob, eff, bseq, localhomtable, ntarget ); // CHUUI
else
- calcimportance_half( njob, eff, bseq, localhomtable );
+ calcimportance_half( njob, eff, bseq, localhomtable, alloclen );
// dontcalcimportance_half( njob, eff, bseq, localhomtable ); // CHUUI
}
=====================================
core/tditeration.c
=====================================
@@ -1406,9 +1406,9 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],
{
counteff_simple( locnjob, topol, len, effarrforlocalhom );
if( ntarget < locnjob )
- calcimportance_target( locnjob, ntarget, effarrforlocalhom, aseq, localhomtable, targetmap, targetmapr );
+ calcimportance_target( locnjob, ntarget, effarrforlocalhom, aseq, localhomtable, targetmap, targetmapr, alloclen );
else
- calcimportance_half( locnjob, effarrforlocalhom, aseq, localhomtable );
+ calcimportance_half( locnjob, effarrforlocalhom, aseq, localhomtable, alloclen );
}
if( weight == 2 )
@@ -1631,9 +1631,9 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],
{
counteff_simple( locnjob, topol, len, effarrforlocalhom );
if( ntarget < locnjob )
- calcimportance_target( locnjob, ntarget, effarrforlocalhom, aseq, localhomtable, targetmap, targetmapr );
+ calcimportance_target( locnjob, ntarget, effarrforlocalhom, aseq, localhomtable, targetmap, targetmapr, alloclen );
else
- calcimportance_half( locnjob, effarrforlocalhom, aseq, localhomtable );
+ calcimportance_half( locnjob, effarrforlocalhom, aseq, localhomtable, alloclen );
}
}
=====================================
core/univscript.tmpl
=====================================
@@ -1,37 +1,27 @@
progs="_PROGS"
+progs="$progs dash_client"
for prog in $progs; do
printf $prog" "
done
make clean
-make CC="$HOME/soft/gcc/usr/local/bin/gcc" CFLAGS="-O3 -m32 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5 -static-libgcc" LIBS="-lm -lpthread -lgcc_eh" ENABLE_MULTITHREAD="-Denablemultithread"
+make CC="clang" CFLAGS="-O3 -arch x86_64 -mmacosx-version-min=10.9 -DMACOSX_DEPLOYMENT_TARGET=10.9" LIBS="-lm -lpthread" ENABLE_MULTITHREAD="-Denablemultithread"
+env CC='clang -O3 -arch x86_64' GOARCH=amd64 GOOS=darwin CGO_ENABLED=0 go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki
for prog in $progs; do
- mv $prog $prog.intel32
+ mv $prog $prog.x86_64
done
make clean
-make CC="$HOME/soft/gcc/usr/local/bin/gcc" CFLAGS="-O3 -m64 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5 -static-libgcc" LIBS="-lm -lpthread -lgcc_eh" ENABLE_MULTITHREAD="-Denablemultithread"
+make CC="clang" CFLAGS="-O3 -arch arm64 -mmacosx-version-min=11.1 -DMACOSX_DEPLOYMENT_TARGET=11.1" LIBS="-lm -lpthread" ENABLE_MULTITHREAD="-Denablemultithread"
+env CC='clang -O3 -arch arm64' GOARCH=arm64 GOOS=darwin CGO_ENABLED=0 go build --ldflags '-extldflags "-static"' dash_client.go # uwagaki
for prog in $progs; do
- mv $prog $prog.intel64
+ mv $prog $prog.arm64
done
-#make clean
-#make CC="gcc-4.0" CFLAGS="-arch ppc64 -m64 -O3 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5" ENABLE_MULTITHREAD=""
-#for prog in $progs; do
-# mv $prog $prog.ppc64
-#done
-#
-#make clean
-#make CC="gcc-4.0" CFLAGS="-arch ppc -m32 -O3 -mmacosx-version-min=10.5 -isysroot/Developer/SDKs/MacOSX10.5.sdk -DMACOSX_DEPLOYMENT_TARGET=10.5" ENABLE_MULTITHREAD=""
-#for prog in $progs; do
-# mv $prog $prog.ppc32
-#done
-
-
set $progs
for prog in $progs; do
# lipo -create $prog.icc $prog.ppc32 $prog.ppc64 -output $prog
# lipo -create $prog.intel64 $prog.intel32 $prog.ppc32 $prog.ppc64 -output $prog
- lipo -create $prog.intel64 $prog.intel32 -output $prog
+ lipo -create $prog.x86_64 $prog.arm64 -output $prog
cp $prog ../binaries
done
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+mafft (7.481-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * New upstream version 7.481
+
+ -- Nilesh Patra <nilesh at debian.org> Sat, 12 Jun 2021 02:06:47 +0530
+
mafft (7.475-1) unstable; urgency=medium
* Team upload.
=====================================
readme
=====================================
@@ -1,6 +1,6 @@
-----------------------------------------------------------------------
MAFFT: a multiple sequence alignment program
- version 7.475, 2020/Nov/23
+ version 7.481, 2021/May/26
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/18fa60ced0c36e9bbb75f1ef3546eb13256cd916...b23f7f4671b1924a83dda55b4a58d4dfc323b470
--
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/compare/18fa60ced0c36e9bbb75f1ef3546eb13256cd916...b23f7f4671b1924a83dda55b4a58d4dfc323b470
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