[med-svn] [Git][med-team/mafft][upstream] New upstream version 7.467
Steffen Möller
gitlab at salsa.debian.org
Fri May 15 12:17:07 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / mafft
Commits:
207670d8 by Steffen Moeller at 2020-05-15T13:14:52+02:00
New upstream version 7.467
- - - - -
6 changed files:
- core/Falign.c
- core/addsingle.c
- core/defs.c
- core/mafft.tmpl
- core/mltaln.h
- readme
Changes:
=====================================
core/Falign.c
=====================================
@@ -1364,6 +1364,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
for( j=0; j<clus2; j++ ) result2[j][0] = 0;
totalscore = 0.0;
*fftlog = -1;
+// reporterr( "\nin Falign(), *fftlog = %d\n", *fftlog );
for( i=0; i<count-1; i++ )
{
*fftlog += 1;
@@ -1580,6 +1581,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
}
#endif
}
+// reporterr( "\nafter Falign(), *fftlog = %d\n", *fftlog );
#if KEIKA
fprintf( stderr, "DP ... done \n" );
@@ -3402,6 +3404,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
for( j=0; j<clus2; j++ ) result2[j][0] = 0;
totalscore = 0.0;
*fftlog = -1;
+// reporterr( "\nin Falign_udpari(), *fftlog = %d\n", *fftlog );
for( i=0; i<count-1; i++ )
{
*fftlog += 1;
@@ -3549,6 +3552,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
}
#endif
}
+
+
+// reporterr( "\nafter Falign_udpari(), *fftlog = %d\n", *fftlog );
+
#if KEIKA
fprintf( stderr, "DP ... done \n" );
#endif
=====================================
core/addsingle.c
=====================================
@@ -1389,7 +1389,8 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
- if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
+// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
else ffttry = 0;
// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (double)len1/fftlog[m1], clus1, (double)len2/fftlog[m2], clus2 );
@@ -2961,7 +2962,7 @@ int main( int argc, char *argv[] )
fprintf( stderr, "norg = %d\n", norg );
fprintf( stderr, "njobc = %d\n", njobc );
// if( norg > 1000 || nadd > 1000 ) use_fft = 0;
- if( norg > 1000 ) use_fft = 0;
+// if( norg > 1000 ) use_fft = 0;
fullseqlen = alloclen = nlenmax*4+1; //chuui!
=====================================
core/defs.c
=====================================
@@ -1,10 +1,10 @@
#include "mltaln.h"
#include "dp.h"
-int TLS commonAlloc1 = 0;
-int TLS commonAlloc2 = 0;
-int TLS **commonIP = NULL;
-int TLS **commonJP = NULL;
+TLS int commonAlloc1 = 0;
+TLS int commonAlloc2 = 0;
+TLS int **commonIP = NULL;
+TLS int **commonJP = NULL;
int nthread = 1;
int nthreadpair = 1;
int randomseed = 0;
@@ -115,7 +115,7 @@ double consweight_multi = 1.0;
double consweight_rna = 0.0;
char RNAscoremtx = 'n';
-char TLS *newgapstr = "-";
+TLS char *newgapstr = "-";
int nalphabets = 26;
int nscoredalphabets = 20;
=====================================
core/mafft.tmpl
=====================================
@@ -1,7 +1,7 @@
#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.464 (2020/Apr/21)"; export version
+version="v7.467 (2020/May/14)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
@@ -2316,11 +2316,8 @@ function removetmpfile() { # for MPI
fi
if [ $anysymbol -eq 1 ]; then
mv orig infile # replaceu wo mukouka
- #else
- # Check sequence here
fi
-# mv infile infile2
-# cat /dev/null > infile
+ sed 's/-//g' infile > dashin # gap nozoku
if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
echo "" 1>&2
@@ -2335,7 +2332,7 @@ function removetmpfile() { # for MPI
fi
echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
- "$prefix/dash_client" -i infile -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
+ "$prefix/dash_client" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
dashres="$?"
if [ $dashres -ne "0" ]; then
echo "Error in DASH" 1>>"$progressfile"
@@ -2348,6 +2345,17 @@ function removetmpfile() { # for MPI
mv ho_excluded dashsequences
fi
+ if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30
+ ndash=`grep -c '>DASH_' dashsequences | head -1`
+# echo "ndash = " $ndash
+ awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted
+ mv _subalignmentstableshifted _subalignmentstable
+ cp dashsequences dashsequences.bk
+ awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2
+ cat infile >> infile2
+ cp infile2 dashsequences
+ fi
+
sed 's/>DASH_/>DASH|/' dashsequences > renamed
mv renamed dashsequences
echo "Done." 1>>"$progressfile"
@@ -2366,54 +2374,11 @@ function removetmpfile() { # for MPI
cat dashsequences > infile
# cat infile2 >> infile
fi
-
-# elif [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
-# mv infile infile2
-# if [ $anysymbol -eq 1 ]; then
-# mv orig orig2
-# cat /dev/null > orig
-# fi
-# cat /dev/null > infile
-#
-# echo "strdir = " 1>>"$progressfile"
-# echo $strdir 1>>"$progressfile"
-#
-# echo "Calling DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/)" 1>>"$progressfile"
-# perl "$prefix/mafftash_premafft.pl" -p pdblist -o ownlist -d "$strdir" 2>>"dasherr"
-# dashres="$?"
-# cat dasherr 1>>"$progressfile"
-#
-# if [ $dashres -ne "0" ]; then
-# echo "Error in DASH" 1>>"$progressfile"
-# exit 1;
-# fi
-# echo "Done." 1>>"$progressfile"
-#
-# seedoffset=`grep -c '^[>|=]' instr | head -1 `
-#
-# echo "# of structures = " 1>>"$progressfile"
-# echo $seedoffset 1>>"$progressfile"
-# mv hat3 hat3.seed
-#
-# if [ $anysymbol -eq 1 ]; then
-# cat instr >> orig
-# "$prefix/replaceu" $seqtype -i instr -o 0 > clean 2>>"$progressfile" || exit 1
-# mv clean infile
-#
-# "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
-# cat orig2 >> orig
-# else
-# cat instr > infile
-# cat infile2 >> infile
-# fi
else
cat /dev/null > hat3.seed
fi
# cat hat3.seed
-
-
-
if [ $mccaskill -eq 1 ]; then
"$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
elif [ $dafs -eq 1 ]; then
=====================================
core/mltaln.h
=====================================
@@ -1,7 +1,6 @@
#define USE_XCED 0
-#define _SVID_SOURCE
-#define _BSD_SOURCE
+#define _XOPEN_SOURCE
#if USE_XCED
#include "config.h"
@@ -37,7 +36,7 @@
-#define VERSION "7.464"
+#define VERSION "7.467"
#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
=====================================
readme
=====================================
@@ -1,6 +1,6 @@
-----------------------------------------------------------------------
MAFFT: a multiple sequence alignment program
- version 7.464, 2020/Apr/21
+ version 7.467, 2020/May/14
http://mafft.cbrc.jp/alignment/software/
katoh at ifrec.osaka-u.ac.jp
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e
--
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e
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