MPI/Makefile

@@ -14,7 +14,7 @@ CFLAGS := -O3
 #CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind
 # CFLAGS := -O0 -g -ipo -no-prec-div -xHost -std=c99
 TARGET_ARCH := 
-LDLIBS := -lm -lrt   # -lrt?
+LDLIBS := -lm -lrt -lpthread  # -lrt?
 
 
 ENABLE_MULTITHREAD := -Denablemultithread

core/MSalignmm.c

@@ -719,6 +719,7 @@ static double MSalignmm_tanni( double **n_dynamicmtx, int icyc, int jcyc, double
 	lgth1 = ien-ist+1;
 	lgth2 = jen-jst+1;
 
+
 #if STOREWM
 	strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
 	strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
@@ -2124,6 +2125,7 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 	nglen1 = seqlen( seq1[0] );
 	nglen2 = seqlen( seq2[0] );
 
+
 #if 0
 	fprintf( stderr, "\n" );
 	for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[%d] at root = %s\n", i, seq1[i] );
@@ -2134,6 +2136,7 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 	lgth1 = strlen( seq1[0] );
 	lgth2 = strlen( seq2[0] );
 
+
 	ll1 = ( (int)(lgth1) ) + 100;
 	ll2 = ( (int)(lgth2) ) + 100;
 

core/Salignmm.c

@@ -819,6 +819,7 @@ static void createfgresult( double **gapfresult, int limk, double eff1, double e
 }
 
 static double Atracking( double *lasthorizontalw, double *lastverticalw, 
+						double fpenalty, double fpenalty_ex,
 						char **seq1, char **seq2, 
                         char **mseq1, char **mseq2, 
                         int **ijp, int icyc, int jcyc,
@@ -876,8 +877,8 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw,
 	else
 	{
 #if 1
-		double fpenalty = (double)penalty;
-		double fpenalty_ex = (double)penalty_ex;
+//		double fpenalty = (double)penalty;
+//		double fpenalty_ex = (double)penalty_ex;
 		double g;
 //		reporterr( "in S, lastverticalw[lgth1-1] = %f\n", lastverticalw[lgth1-1] );
 //		reporterr( "in S, lasthorizontalw[lgth2-1] = %f\n", lasthorizontalw[lgth2-1] );
@@ -1066,7 +1067,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw,
 	return( wm );
 }
 
-double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, int firstmem, int calledbyfulltreebase, double **cpmxchild0, double **cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 )
+double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, int firstmem, int calledbyfulltreebase, double **cpmxchild0, double **cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 )
 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 {
 
@@ -1087,7 +1088,7 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 	double *currentw, *previousw;
 //	double fpenalty = (double)penalty;
 #if USE_PENALTY_EX
-	double fpenalty_ex = (double)penalty_ex;
+	double fpenalty_ex = (double)penalty_ex_l;
 #endif
 #if 1
 	double *wtmp;
@@ -1121,7 +1122,7 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 	double *gapfreq1pt;
 	static TLS double *gapfreq2;
 	double *gapfreq2pt;
-	double fpenalty = (double)penalty;
+	double fpenalty = (double)penalty_l;
 	double fpenalty_shift = (double)penalty_shift;
 	double *fgcp2pt;
 	double *ogcp2pt;
@@ -2050,7 +2051,7 @@ fprintf( stderr, "\n" );
 	else
 	{
 //		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, eff1, eff2, cpmxresult, cpmx1pt, cpmx2pt, gapfreq1pt, gapfreq2pt, ogcp1opt, ogcp2opt, fgcp1opt, fgcp2opt, orieff1, orieff2, (cpmx1pt!=cpmx1), (cpmx2pt!=cpmx2) );
-		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, &gt1, &gt2 );
+		wmo = Atracking( currentw, lastverticalw, fpenalty, fpenalty_ex, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, &gt1, &gt2 );
 		if( !tailgp ) wm = wmo;
 	}
 
@@ -2194,7 +2195,7 @@ double A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, in
 }
 
 
-double A__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+double A__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 {
 
@@ -2211,7 +2212,7 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic
 	double *currentw, *previousw;
 //	double fpenalty = (double)penalty;
 #if USE_PENALTY_EX
-	double fpenalty_ex = (double)penalty_ex;
+	double fpenalty_ex = (double)penalty_ex_l;
 #endif
 #if 1
 	double *wtmp;
@@ -2240,7 +2241,7 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic
 	static TLS int orlgth1 = 0, orlgth2 = 0;
 	static TLS double *gapfreq1;
 	static TLS double *gapfreq2;
-	double fpenalty = (double)penalty;
+	double fpenalty = (double)penalty_l;
 	double fpenalty_shift = (double)penalty_shift;
 	double *fgcp2pt;
 	double *ogcp2pt;
@@ -3041,7 +3042,7 @@ fprintf( stderr, "\n" );
 	else
 	{
 //		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.0, 0.0, 1, 1 ); // NULL x 11 ha atode awaseru.
-		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL);
+		wmo = Atracking( currentw, lastverticalw, fpenalty, fpenalty_ex, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL);
 		if( !tailgp ) wm = wmo;
 	}
 

core/addfunctions.c

@@ -86,7 +86,7 @@ void profilealignment2( int n0, int n2, char **aln0, char **aln2, int alloclen,
 	if( alg == 'M' )
 		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
 	else
-		A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
+		A__align( n_dis_consweight_multi, penalty, penalty_ex, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
 
 	newlen = strlen( aln0[0] );
 
@@ -211,7 +211,7 @@ static void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1,
 	if( alg == 'M' )
 		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
 	else
-		A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
+		A__align( n_dis_consweight_multi, penalty, penalty_ex, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1
 
 	newlen = strlen( aln0[0] );
 

core/addsingle.c

@@ -1397,7 +1397,7 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
 			{
 				imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, NULL, 1, topol[l][0], topol[l][1], NULL, NULL, NULL, -1, 0 );
 				if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
-				pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
+				pscore = A__align( n_dis_consweight_multi, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
 			}
 			else if( alg == 'Q' )
 			{
@@ -1430,7 +1430,7 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
 					pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, NULL, NULL, NULL, 0.0, 0.0 );
 					break;
 				case( 'A' ):
-					pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
+					pscore = A__align( n_dis_consweight_multi, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
 					break;
 				default:
 					ErrorExit( "ERROR IN SOURCE FILE" );
@@ -1974,7 +1974,7 @@ static void	*addsinglethread( void *arg )
 		if( mseq1 ) free( mseq1 ); mseq1 = NULL;
 		if( mseq2 ) free( mseq2 ); mseq2 = NULL;
 		Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
-		A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+		A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 		if( commonIP ) FreeIntMtx( commonIP );
 		commonIP = NULL;
 		commonAlloc1 = commonAlloc2 = 0;

core/dash_client.go

@@ -16,7 +16,7 @@ import(
     "time"
 )
 
-var VersionNumber = 1.0
+var VersionNumber = 1.1
 var Debug = false
 var NumberOfQueryTries = 12
 var HTTPClient = &http.Client{}
@@ -939,6 +939,7 @@ func filter_sequences_and_hat3(sequence_file_path string, hat3_path string,
     //Write Cleaned Sequences
     new_sequence_file, err := os.Create(sequence_file_path)
     check(err)
+    defer new_sequence_file.Close()
     for _, old_index := range(existing_hat3_indexes) {
         sequence := sequence_data[old_index]
         sequence_lines := fmt.Sprintf(">%s\n%s", sequence.Label, sequence.Sequence)
@@ -1346,6 +1347,7 @@ func main() {
     fmt.Println("Combining original sequences with DASH sequences...")
     dash_sequences := ParseFASTA(sequences_output_path)
     final_sequence_file, err := os.Create(sequences_output_path)
+    check(err)
     for _, sequence := range(dash_sequences) {
         fmt.Fprintln(final_sequence_file,
             fmt.Sprintf(">%s\n%s", sequence.Label, sequence.Sequence))

core/functions.h

@@ -147,13 +147,14 @@ extern double Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *ef
 extern double Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, double **map );
 extern double MSalign11( char **seq1, char **seq2, int alloclen );
 //extern double rnalocal( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, RNApair **pair );
-extern double A__align( double **scoringmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp, int firstmem, int calledby, double **cpmxchild0, double **cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 );
-extern double A__align_variousdist( int **which, double ***scoringmatrices, double **dummtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp );
+extern double A__align( double **scoringmtx, int penalty, int penalty_ex, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp, int firstmem, int calledby, double **cpmxchild0, double **cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 );
+extern double A__align_variousdist( int **which, double ***scoringmatrices, double **dummtx, int penalty, int penalty_ex, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp );
 extern double A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int *gapmap1, int *gapmap2 );
 extern double translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen );
 extern double Fgetlag( double **scoringmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, int    clus1, int    clus2, int alloclen );
 extern double Falign( int **whichmtx, double ***scoringmatrices, double **scoreingmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int *fftlog, int *, int, int * );
 extern double Falign_udpari_long( int **whichmtx, double ***scoringmatrices, double **scoringmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int *fftlog );
+extern double Falign_givenanchors( ExtAnch *extanch, int **whichmtx, double ***scoringmatrices, double **scoringmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int *fftlog );
 double Falign_localhom( int **which, double ***scoringmatrices, double **scoreingmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int constraint, double *totalimpmatch, int *gapmap1, int *gapmap2, int *chudanpt, int chudanref, int *chudanres );
 extern double part_imp_match_out_sc( int i1, int j1 );
 extern void part_imp_match_init_strict( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, char *swaplist, int forscore, int *memlist1, int *memlist2 );
@@ -423,3 +424,4 @@ extern void limitlh( int *uselh, Lennum *in, int size, int limit );
 
 extern double distdp_noalign( char *s1, char *s2, double selfscore1, double selfscore2, int alloclen ); // tbfast.c kara yobareru
 extern void getweightfromname( int n, double *w, char **name );
+extern void readexternalanchors( ExtAnch **extanch, int nseq, int *nogaplen );

core/io.c

@@ -60,13 +60,45 @@ char creverse( char f )
 	return( table[(int)f] );
 }
 
+static int countc( char *s, char q )
+{
+	int v = 0;
+	while( *s )
+		if( *s++ == q ) v++;
+	return( v );
+}
+
+static void ttou( char *s )
+{
+	int v = 0;
+	while( *s )
+	{
+		if( *s == 't' ) *s = 'u';
+		else if( *s == 'T' ) *s = 'U';
+		s++;
+	}
+}
+
 void sreverse( char *r, char *s )
 {
+	int numt = countc( s, 't' ) + countc( s, 'T' );
+	int numu = countc( s, 'u' ) + countc( s, 'U' );
+
+//	reporterr( "numt=%d, numu=%d\n", numt, numu );
+//	reporterr( "s=%s\n", s );
+
 	r += strlen( s );
 	*r-- = 0;
 	while( *s )
 		*r-- = creverse( *s++ );
 //		*r-- = ( *s++ );
+	if( numu > numt )
+	{
+//		reporterr( "RNA!\n" );
+//		reporterr( "r before ttou =%s\n", r );
+		ttou( r+1 );
+//		reporterr( "r after ttou =%s\n", r );
+	}
 }
 
 void gappick_samestring( char *seq )
@@ -6157,7 +6189,7 @@ void use_getrusage(void)
 	if (getrusage(RUSAGE_SELF, &r) != 0) {
 		/*Failure*/
 	}
-	fprintf(stderr, "maxrss = %ld MB\n", r.ru_maxrss/1000);
+	fprintf(stderr, "\nmaxrss = %ld MB\n", r.ru_maxrss/1000);
 }
 
 #endif
@@ -6243,3 +6275,73 @@ void commongappick( int nseq, char **seq )
 
 #endif
 }
+
+void readexternalanchors( ExtAnch **extanch, int nseq, int *nogaplen )
+{
+	FILE *fp;
+	int size, lineno;
+	char buf[10000];
+	fp = fopen( "_externalanchors", "r" );
+
+	if( fp == NULL )
+	{
+		reporterr( "Cannot open _externalanchors\n" );
+		exit( 1 );
+	}
+
+	size = 0;
+	lineno = 0;
+	while( 1 )
+	{
+		lineno++;
+//		reporterr( "size = %d\n", size );
+		fgets( buf, 9999, fp );
+		if( feof( fp ) ) break;
+
+		if( buf[0] == '#' ) continue;
+
+//		reporterr( "buf=%s\n", buf );
+		*extanch = realloc( *extanch, sizeof( ExtAnch ) * (size+2) );
+		if( *extanch == NULL )
+		{
+			reporterr( "Cannot realloc *extanch\n" );
+			exit( 1 );
+		}
+
+		sscanf( buf, "%d %d %d %d %d %d %d", &(((*extanch)+size)->i), &(((*extanch)+size)->j), &(((*extanch)+size)->starti), &(((*extanch)+size)->endi), &(((*extanch)+size)->startj), &(((*extanch)+size)->endj), &(((*extanch)+size)->score) );
+//		reporterr( "i=%d, j=%d, %d-%d, %d-%d, score=%d\n", (*extanch)[size].i, (*extanch)[size].j, (*extanch)[size].starti, (*extanch)[size].endi, (*extanch)[size].startj, (*extanch)[size].endj, (*extanch)[size].score );
+
+		((*extanch)+size)->i -= 1; // 1-origin -> 0-origin
+		((*extanch)+size)->j -= 1; // 1-origin -> 0-origin
+		((*extanch)+size)->starti -= 1; 
+		((*extanch)+size)->startj -= 1;
+		((*extanch)+size)->endi -= 1;
+		((*extanch)+size)->endj -= 1;
+
+		if( (*extanch)[size].i >= nseq || (*extanch)[size].j >= nseq )
+		{
+			reporterr( "\nOut of range?  The input file has %d sequences but pair %d-%d was specified in line %d.\nNote that sequence IDs are counted from 1.\n", nseq, (*extanch)[size].i+1, (*extanch)[size].j+1, lineno );
+			exit( 1 );
+		}
+		if( (*extanch)[size].i >= (*extanch)[size].j )
+		{
+			reporterr( "\nFormat problem?  \"%d %d\" in line %d.\nThe sequence id of the first column must be less than the second.\n", (*extanch)[size].i+1, (*extanch)[size].j+1, lineno );
+			exit( 1 );
+		}
+		if( (*extanch)[size].starti > nogaplen[(*extanch)[size].i] )
+		{
+			reporterr( "\nOut of range?  len(seq%d)=%d, but anchor=%d in line %d.\nNote that position is counted from 1.\n", (*extanch)[size].i+1, nogaplen[(*extanch)[size].i], (*extanch)[size].starti+1, lineno );
+			exit( 1 );
+		}
+		if( (*extanch)[size].startj > nogaplen[(*extanch)[size].j] )
+		{
+			reporterr( "\nOut of range?  len(seq%d)=%d, but anchor=%d in line %d.\nNote that position is counted from 1.\n", (*extanch)[size].j, nogaplen[(*extanch)[size].j]+1, (*extanch)[size].startj+1, lineno );
+			exit( 1 );
+		}
+
+		size++;
+		(*extanch)[size].i = (*extanch)[size].j = -1;
+
+	}
+	fclose( fp );
+}

core/mafft-profile.c

@@ -262,7 +262,7 @@ void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char
 		if( alg == 'M' )
 			pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, NULL, NULL, NULL, 0.0, 0.0 );
 		else
-			pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+			pscore = A__align( n_dis_consweight_multi, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 	}
 #if DEBUG
 		time2 = getrusage_sec();

core/mafft.tmpl

 #! /bin/bash 
 er=0;
 myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.429 (2019/Jul/1)"; export version
+version="v7.453 (2019/Nov/8)"; export version
 LANG=C; export LANG
 os=`uname`
 progname=`basename "$0"`
@@ -214,6 +214,7 @@ dafs=$defaultdafs
 mccaskill=$defaultmccaskill
 contrafold=$defaultcontrafold
 progressfile="/dev/stderr"
+anchorfile="/dev/null"
 debug=0
 sw=0
 algopt=$defaultalgopt
@@ -530,6 +531,17 @@ if [ $# -gt 0 ]; then
 		elif [ "$1" = "--out" ]; then 
 			shift   
 			outputfile="$1"
+		elif [ "$1" = "--anchors" ]; then 
+			shift
+			anchorfile="$1"
+			anchoropt=" -l "
+#			memopt=" -M -B "      # ato de kentou
+#			memopt=" -N "         # no memsave
+			if [ ! -e "$anchorfile" ]; then
+				echo "Cannot open $anchorfile" 1>&2
+				echo "" 1>&2
+				exit
+			fi
 		elif [ "$1" = "--thread" ]; then 
 			shift
 			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
@@ -1047,6 +1059,7 @@ function removetmpfile() { # for MPI
 			cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_lara.params"
 			cat "$pdblist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/pdblist"
 			cat "$ownlist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist"
+			cat "$anchorfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
 
 			SAVEIFS=$IFS
 			IFS='\n'
@@ -1878,19 +1891,19 @@ function removetmpfile() { # for MPI
 			fi
 		fi
 		if [ $iterate -gt 0 ]; then
-			echo 'Iterative refinment is not supported for --'$treeext  1>>"$progressfile"
+			echo 'Iterative refinment is not supported for --large or --'$treeext  1>>"$progressfile"
 			echo '' 1>>"$progressfile"
 			exit 1
 		fi
 		if [ $fragment -ne 0 ]; then
-			echo '--addfragments, --addfull or --addlong is not yet supported for --'$treeext  1>>"$progressfile"
+			echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext  1>>"$progressfile"
 			echo "Use --add newsequences --$treeext" 1>>"$progressfile"
 			echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile"
 			echo '' 1>>"$progressfile"
 			exit 1
 		fi
 		if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2
-			echo '--merge is not yet supported for --'$treeext  1>>"$progressfile"
+			echo '--merge is not yet supported for --large or --'$treeext  1>>"$progressfile"
 			echo "Use --merge without --"$treeext 1>>"$progressfile"
 			echo '' 1>>"$progressfile"
 			exit 1
@@ -1925,6 +1938,7 @@ function removetmpfile() { # for MPI
 			bunkatsuopt=" -B "  # fftnsi demo bunktasu shinai
 			if [ "$add2ndhalfarg" != " " ]; then
 				if [ $auto -eq 1 -o $iterate -gt 0 ]; then
+					echo '' 1>>"$progressfile"
 					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
 					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
 					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
@@ -1934,9 +1948,18 @@ function removetmpfile() { # for MPI
 			fi
 		fi
 		
+
 #		cycle=1 # chuui 2014Aug19
 #		iterate=0
 #		treealg=" -q "  ## 2012/01/24  ## removed 2012/02/06
+	else
+		if [ "$add2ndhalfarg" != " " ]; then
+			echo '' 1>>"$progressfile"
+			echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile"
+			echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
 	fi
 
 
@@ -2093,15 +2116,15 @@ function removetmpfile() { # for MPI
 	fi
 
 	if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
-		outputopt=" -c $strategy -r _order$$ $f2clext "
+		outputopt=" -c $strategy -r $TMPFILE/order $f2clext "
 	elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
 		outputopt=" -c $strategy  $f2clext "
 	elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
-		outputopt=" -y -r _order$$ "
+		outputopt=" -y -r $TMPFILE/order "
 	elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
 		outputopt=" -y "
 	elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
-		outputopt=" -f -r _order$$ "
+		outputopt=" -f -r $TMPFILE/order "
 	else
 		outputopt="-f"
 	fi
@@ -2524,7 +2547,7 @@ function removetmpfile() { # for MPI
 			if [ $fragment -ne 0 ]; then 
 				"$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
 			else
-				"$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist  -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg < infile   > pre 2>>"$progressfile" || exit 1
+				"$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist  -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg $anchoropt < infile   > pre 2>>"$progressfile" || exit 1
 				mv hat3.seed hat3
 			fi
 		fi
@@ -2542,7 +2565,7 @@ function removetmpfile() { # for MPI
 		done
 		if [ $iterate -gt 0 ]; then
 			if [ $distance = "ktuples" ]; then
-			    "$prefix/dndpre" $model -M 2 -C $numthreads < pre     > /dev/null 2>>"$progressfile" || exit 1
+			    "$prefix/dndpre" $seqtype $model -M 2 -C $numthreads < pre     > /dev/null 2>>"$progressfile" || exit 1
 			fi
 			"$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel  $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof  -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy  $scoreoutarg  -K $nadd < pre     > /dev/null 2>>"$progressfile" || exit 1
 		fi
@@ -2653,13 +2676,13 @@ function removetmpfile() { # for MPI
 
 	if [ "$outputopt" != "-f" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu.
 #		ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode
-		cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru
+#		cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru
 		if [ "$outputfile" = "" ]; then
 			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1
 		else
 			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1
 		fi
-		rm _order$$
+#		rm _order$$
 	else
 		if [ "$outputfile" = "" ]; then
 			cat < "$TMPFILE/pre" || exit 1

core/makedirectionlist.c

@@ -857,6 +857,7 @@ int main( int argc, char *argv[] )
 
 		reporterr( "Step 1/2\n" );
 
+
 		if( !dodp )
 		{
 			if( nadd )
@@ -879,7 +880,6 @@ int main( int argc, char *argv[] )
 				istart = 0;
 			for( i=istart; i<njob; i++ ) 
 			{
-
 				gappick0( tmpseq, seq[i] );
 				strcpy( seq[i], tmpseq );
 				sreverse( revseq, tmpseq );

core/mltaln.h

@@ -37,7 +37,7 @@
 
 
 
-#define VERSION "7.429"
+#define VERSION "7.453"
 #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
@@ -321,7 +321,16 @@ typedef struct _pairnum
 	int n1;
 } Pairnum;
 
-
+typedef struct _extanch
+{
+	int i;
+	int j;
+	int starti;
+	int endi;
+	int startj;
+	int endj;
+	int score;
+} ExtAnch;
 
 #include "fft.h"
 #include "dp.h"

core/serial.c

@@ -360,7 +360,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char
 					{
 						if( l < 500 || l % 100 == 0 ) if( cpmxchild1 || cpmxchild0 ) reporterr(       " h" );
 //						reporterr(       "\n\n %d - %d (%d x %d) : \n", topol[l][0][0], topol[l][1][0], clus1, clus2 );
-						pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
+						pscore = A__align( dynamicmtx, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
 					}
 
 					break;
@@ -510,7 +510,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char
 #endif
 	Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
 	Falign_udpari_long( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
-	A__align( NULL,  NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+	A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 	D__align( NULL,  NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 	G__align11( NULL, NULL, NULL, 0, 0, 0 ); // iru?
 	free( effarr1 );
@@ -531,7 +531,7 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char
 
 	Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
 	Falign_udpari_long( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
-	A__align( NULL,  NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+	A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 	D__align( NULL,  NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 	G__align11( NULL, NULL, NULL, 0, 0, 0 ); // iru?
 	if( effarr1 ) free( effarr1 ); effarr1 = NULL;

core/setdirection.c

@@ -137,6 +137,7 @@ int main( int argc, char *argv[] )
 		}
 		if( line[1] == 'R' )
 		{
+
 			directions[i] = 'R';
 			sreverse( tmpseq, seq[i] );
 			strcpy( seq[i], tmpseq );

core/splittbfast.c

@@ -1050,7 +1050,7 @@ static void pairalign( int nseq, int *nlen, char **seq, int *mem1, int *mem2, do
 				else
 				{
 //					fprintf( stderr, "%d-%d", clus1, clus2 );
-					pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+					pscore = A__align( n_dis_consweight_multi, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 				}
 				break;
 			default:

core/tbfast.c

@@ -891,7 +891,7 @@ static void *treebasethread( void *arg ) // seed && compacttree==3 niha taioushi
 			commonIP = NULL;
 			Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
 			Falign_udpari_long( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
-			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+			A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 			D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 			partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
 			G__align11( NULL, NULL, NULL, 0, 0, 0 ); // iru?
@@ -1108,7 +1108,7 @@ static void *treebasethread( void *arg ) // seed && compacttree==3 niha taioushi
 			{
 				imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, swaplist, 1, localmem[0], localmem[1], uselh, NULL, NULL, (compacttree==3)?l:-1, 0 ); // seedinlh, nfiles ni ha taiou shiteinai
 				if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
-				pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxhist mitaiou
+				pscore = A__align( dynamicmtx, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxhist mitaiou
 			}
 			if( alg == 'd' )
 			{
@@ -1147,7 +1147,7 @@ static void *treebasethread( void *arg ) // seed && compacttree==3 niha taioushi
 					pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxhist mitaiou
 					break;
 				case( 'A' ):
-					pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxhist mitaiou
+					pscore = A__align( dynamicmtx, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxhist mitaiou
 					break;
 				case( 'd' ):
 					pscore = D__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
@@ -1590,7 +1590,7 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq
 #if REPORTCOSTS
 //				reporterr(       "\n\n %d - %d (%d x %d) : \n", topol[l][0][0], topol[l][1][0], clus1, clus2 );
 #endif
-				pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
+				pscore = A__align( dynamicmtx, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
 			}
 			if( alg == 'd' )
 			{
@@ -1629,7 +1629,7 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq
 					pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
 					break;
 				case( 'A' ):
-					pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
+					pscore = A__align( dynamicmtx, penalty, penalty_ex, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, localmem[0][0], 1, cpmxchild0, cpmxchild1, cpmxhist+l, orieff1, orieff2 );
 					break;
 				case( 'd' ):
 					pscore = D__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
@@ -1766,7 +1766,7 @@ void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq
 	free( effarr2_kozo );
 	Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
 	D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
-	A__align( NULL,  NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+	A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 	imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, 0, 0 );
 	imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, 0, 0 );
 	FreeCommonIP();

debian/changelog

+mafft (7.453-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.4.1
+  * Trim trailing whitespace.
+  * Use secure URI in Homepage field.
+  * Set fields Upstream-Name, Upstream-Contact in debian/copyright.
+  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 21 Nov 2019 17:27:17 +0100
+
 mafft (7.429-1) unstable; urgency=medium
 
   * Team upload.
@@ -389,4 +401,3 @@ mafft (6.240-1) unstable; urgency=low
   * Initial release (Closes: #409640)
 
  -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat,  9 Jun 2007 12:06:43 +0900
-

debian/control

@@ -5,10 +5,10 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 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/
+Homepage: https://mafft.cbrc.jp/alignment/software/
 
 Package: mafft
 Architecture: any