JWS-112 Bumping version of Mafft to version 7.310.

[jabaws.git] / binaries / src / mafft / core / replaceu.c

diff --git a/binaries/src/mafft/core/replaceu.c b/binaries/src/mafft/core/replaceu.c
index 40be746..6df0e60 100644 (file)
--- a/binaries/src/mafft/core/replaceu.c
+++ b/binaries/src/mafft/core/replaceu.c
@@ -27,6 +27,7 @@ void arguments( int argc, char *argv[] )
 
        seedoffset = 0;
        inputfile = NULL;
+       dorp = NOTSPECIFIED;
 
     while( --argc > 0 && (*++argv)[0] == '-' )
        {
@@ -35,7 +36,7 @@ void arguments( int argc, char *argv[] )
             switch( c )
             {
                                case 'o':
-                                       seedoffset = atoi( *++argv );
+                                       seedoffset = myatoi( *++argv );
                                        fprintf( stderr, "seedoffset = %d\n", seedoffset );
                                        --argc;
                                        goto nextoption;
@@ -44,6 +45,12 @@ void arguments( int argc, char *argv[] )
                                        fprintf( stderr, "inputfile = %s\n", inputfile );
                                        --argc;
                                        goto nextoption;
+                               case 'D':
+                                       dorp = 'd';
+                                       break;
+                               case 'P':
+                                       dorp = 'p';
+                                       break;
                 default:
                     fprintf( stderr, "illegal option %c\n", c );
                     argc = 0;
@@ -87,7 +94,7 @@ int main( int argc, char *argv[] )
                infp = stdin;
 
 
-       dorp = NOTSPECIFIED;
+//     dorp = NOTSPECIFIED;
        getnumlen_casepreserve( infp, &nlenmin );
 
        fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
@@ -125,7 +132,7 @@ int main( int argc, char *argv[] )
        }
        else
        {
-               usual = "ATGCUatgcu-";
+               usual = "ATGCUatgcuBDHKMNRSVWYXbdhkmnrsvwyx-";
                replace_unusual( njob, seq, usual, 'n', tolower );
        }
        
@@ -133,7 +140,7 @@ int main( int argc, char *argv[] )
 
        for( i=0; i<njob; i++ )
        {
-               fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
+               fprintf( stdout, ">_os_%d_oe_%s\n", i+seedoffset, name[i]+1 );
                fprintf( stdout, "%s\n", seq[i] );
        }