PRIMER (VMS)

[Christoph Gartmann]

In <2ib1mb$hi9 at hermod.uio.no> rodrigol at biomaster.uio.no writes:

> Please port all relevant fixes as I'm sure a lot of people are
> interested. Since support for the program is not exsistant and
> 'potential' updates are not available, the user community is left
> to it's own mercy and that of people like you and Liz. 

I hope that the rest is self explaining. The version here is V0.5, is
there a newer one?

************
File DISK11:[PRIMER]TEXT.C;1
  116   
/* Program exits if no sample sequence file name given - Liz Cowe, Sept 93 */
/*      gets(line); while(line[0] == '\0' || line[0] == '\n') gets(line);  */
/*      sscanf(line,"%s",sequence_file_name);                              */
        gets(line);                                               
        if(sscanf(line,"%s",sequence_file_name) != 1 ) { exit(1); }
                                                                     
        if((fp = fopen(sequence_file_name,"r")) == NULL) {           
	  printf("*** error: can't open %s\n",sequence_file_name); test1 = 1; 
  124
******
File DISK11:[PRIMER]TEXT.C_ORIGINAL;1
  116
        gets(line); while(line[0] == '\0' || line[0] == '\n') gets(line);
	sscanf(line,"%s",sequence_file_name);
	if((fp = fopen(sequence_file_name,"r")) == NULL) { 
	  printf("*** error: can't open %s\n",sequence_file_name); test1 = 1; 
  119
************
************
File DISK11:[PRIMER]TEXT.C;1
 1380   
/* Was returning 0 if accepted default for num_terminators - Liz Cowe, Sep 93 */
/*    line[0] = '\0'; gets(line); i = 0; num = 0;                             */
/*    n = sscanf(line,"%d",&num);                                             */
/*    if(n <= 0) num = 0;                                                     */
/*    else if(num > 3) { printf("***clamping for 3 bases\n"); num = 3;        */
    line[0] = '\0'; gets(line);                                    
    if(sscanf(line,"%d",&num) == 1) { num_terminators = num; }
    if(num_terminators > 3) { printf("***clamping for 3 bases\n");
       num_terminators = 3; }
        
    if(num_terminators == 1) { strcpy(terminator[0],"C");
       strcpy(terminator[1],"G"); strcpy(terminator[2],""); } 
    else if(num_terminators == 2) { strcpy(terminator[0],"CC");
       strcpy(terminator[1],"CG"); strcpy(terminator[2],"GC");
       strcpy(terminator[3],"GG"); strcpy(terminator[4],""); }
    else if(num_terminators == 3) { strcpy(terminator[0],"CCC");
       strcpy(terminator[1],"CCG"); strcpy(terminator[2],"CGC");
       strcpy(terminator[3],"CGG"); strcpy(terminator[4],"GCC");
       strcpy(terminator[5],"GCG"); strcpy(terminator[6],"GGC");
       strcpy(terminator[7],"GGG"); strcpy(terminator[8],""); }
    else { strcpy(terminator[0],""); }
/*    num_terminators = num;*/
 1403   
******
File DISK11:[PRIMER]TEXT.C_ORIGINAL;1
 1375
    line[0] = '\0'; gets(line); i = 0; num = 0; 
    n = sscanf(line,"%d",&num);
    if(n <= 0) num = 0;
    else if(num > 3) { printf("***clamping for 3 bases\n"); num = 3; }

    if(num == 1) { strcpy(terminator[0],"C"); strcpy(terminator[1],"G");
		    strcpy(terminator[2],"");
    } else if(num == 2) { strcpy(terminator[0],"CC"); strcpy(terminator[1],"CG");
			   strcpy(terminator[2],"GC"); strcpy(terminator[3],"GG"); 
			   strcpy(terminator[4],"");
    } else if(num == 3) { strcpy(terminator[0],"CCC"); strcpy(terminator[1],"CCG");
			   strcpy(terminator[2],"CGC"); strcpy(terminator[3],"CGG");
			   strcpy(terminator[4],"GCC"); strcpy(terminator[5],"GCG");
			   strcpy(terminator[6],"GGC"); strcpy(terminator[7],"GGG");
			   strcpy(terminator[8],""); 
    } else { strcpy(terminator[0],""); }
    num_terminators = num;
 1392   
************
************



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