## 
## Patch to readseq to allow input sequence symbols to be translated
## to different output sequence symbols.  This has not been tested,
## as of 22 Dec 94.  D.Gilbert
##

diff -bwrc old/Makefile rtrans/Makefile
*** old/Makefile	Thu Dec 22 08:58:41 1994
--- rtrans/Makefile	Thu Dec 22 08:58:31 1994
***************
*** 13,21 ****
  CFLAGS=
  #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
  #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
  
  SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
! DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
  
  
  # NCBI toolkit support for ASN.1 reader
--- 13,23 ----
  CFLAGS=  
  #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum 
  #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+ #CFLAGS= -DTRANSLATE # if you want option to translate certain input sequence symbols
+ #    to a different output sequence symbols
  
  SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
! DOCS= Readme readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
  
  
  # NCBI toolkit support for ASN.1 reader


diff -bwrc old/readseq.c rtrans/readseq.c
*** old/readseq.c	Thu Dec 22 08:58:41 1994
--- rtrans/readseq.c	Thu Dec 22 09:01:05 1994
***************
*** 338,343 ****
--- 338,347 ----
    fprintf(stderr, "    -o[utput=]out.seq  redirect Output\n");
    fprintf(stderr, "    -p[ipe]        Pipe (command line, <stdin, >stdout)\n");
    fprintf(stderr, "    -r[everse]     change to Reverse-complement\n");
+ #ifdef TRANSLATE
+   fprintf(stderr, "    -t[ranslate=]io translate input symbol [i] to output symbol [o] \n");
+   fprintf(stderr, "                    use several -tio to translate several symbols \n");
+ #endif
    fprintf(stderr, "    -v[erbose]     Verbose progress\n");
    fprintf(stderr, "    -f[ormat=]#    Format number for output,  or\n");
    fprintf(stderr, "    -f[ormat=]Name Format name for output:\n");
***************
*** 474,479 ****
--- 478,486 ----
    foo = NULL;
  
    gPrettyInit(gPretty);
+ #ifdef TRANSLATE
+   gTranslateInit();
+ #endif
  }
  
  
***************
*** 590,595 ****
--- 597,615 ----
        outform = parseformat( sparam);
        return kOptOkay;
        }
+ 
+ #ifdef TRANSLATE
+     if (checkopt( false, sopt, "-translate", 3)) {/* -translate=io */
+       if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
+ 			if (*sparam) gTranslate[*sparam]= sparam[1];
+       return kOptOkay;
+       }
+     if (checkopt( false, sopt, "-t", 2)) {  /* shorthand is -tio */
+       if (*sparam==0) sparam= sopt+2;
+ 			if (*sparam) gTranslate[*sparam]= sparam[1];
+       return kOptOkay;
+       }
+ #endif
  
      if (checkopt( false, sopt, "-output", 3)) {/* -output=myseq */
        if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }


diff -bwrc old/ureadseq.c rtrans/ureadseq.c
*** old/ureadseq.c	Thu Dec 22 08:58:41 1994
--- rtrans/ureadseq.c	Thu Dec 22 09:01:43 1994
***************
*** 162,168 ****
--- 162,172 ----
            }
          else V->seq = ptr;
          }
+ #ifdef TRANSLATE
+       V->seq[(V->seqlen)++] = gTranslate[*s];
+ #else
        V->seq[(V->seqlen)++] = *s;
+ #endif
        }
      s++;
      }


diff -bwrc old/ureadseq.h rtrans/ureadseq.h
*** old/ureadseq.h	Thu Dec 22 08:58:41 1994
--- rtrans/ureadseq.h	Thu Dec 22 08:58:28 1994
***************
*** 113,118 ****
--- 113,126 ----
  extern  prettyopts  gPretty;
  #endif
  
+ #ifdef TRANSLATE
+ #ifdef UREADSEQ_G
+ char  gTranslate[256];
+ #else
+ extern char  gTranslate[256];
+ #endif
+ #define gTranslateInit() { short c; for(c=0; c<256; c++) gTranslate[c]= c; }
+ #endif
  
  #ifdef __cplusplus
  extern "C" {