23 files changed, 128 insertions, 125 deletions

diff --git a/biology/mapm3/files/patch-Makefile b/biology/mapm3/files/patch-Makefile
index 35bf5e83a6c8..59f0c326a75a 100644
--- a/biology/mapm3/files/patch-Makefile
+++ b/biology/mapm3/files/patch-Makefile
@@ -1,5 +1,5 @@
---- Makefile.orig	1993-02-10 07:12:59.000000000 +0100
-+++ Makefile	2014-01-12 18:47:03.605582463 +0100
+--- Makefile.orig	1993-02-10 06:12:59 UTC
++++ Makefile
 @@ -16,6 +16,7 @@
  ####
  #### For Macs with A/UX, use:	SYS= -D_SYS_AUX
@@ -17,7 +17,7 @@
  
  #### Next define the system libraries to link with Mapmaker. On SunOS, Ultrix
  #### and other vanilla-ish BSD systems, the correct setting is:
-@@ -70,9 +71,11 @@
+@@ -70,9 +71,11 @@ DIR= /usr/local/bin
  #### (see the end of readline/readline.c). Readline will not compile on
  #### A/UX without using GCC instead of A/UX's cc (because it needs alloca).
  
@@ -32,7 +32,7 @@
  
  #### Now we specify the commands used to compile MAPMAKER.  The stuff
  #### below works on Sun SPARCStations running SunOS 4.1.x (aka Solaris 1.x)
-@@ -82,8 +85,8 @@
+@@ -82,8 +85,8 @@ GNU_LIBS= -L$(RDLN) -lreadline
  #### person at your site should be able to figure out what to do almost
  #### trivially. See the file INSTALL.ME for details. 
  
diff --git a/biology/mapm3/files/patch-lib-iolib.c b/biology/mapm3/files/patch-lib-iolib.c
index 4d845b2f6321..957c3ad9369d 100644
--- a/biology/mapm3/files/patch-lib-iolib.c
+++ b/biology/mapm3/files/patch-lib-iolib.c
@@ -1,6 +1,6 @@
---- lib/iolib.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/iolib.c	2008-03-23 15:39:56.000000000 +0000
-@@ -299,7 +299,7 @@
+--- lib/iolib.c.orig	1993-02-09 16:35:24 UTC
++++ lib/iolib.c
+@@ -299,7 +299,7 @@ int length;
  }
  
  
diff --git a/biology/mapm3/files/patch-lib-iolib.h b/biology/mapm3/files/patch-lib-iolib.h
index c753073dc5aa..9407dd6cc768 100644
--- a/biology/mapm3/files/patch-lib-iolib.h
+++ b/biology/mapm3/files/patch-lib-iolib.h
@@ -1,6 +1,6 @@
---- lib/iolib.h.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/iolib.h	2008-04-03 20:00:49.000000000 +0000
-@@ -53,9 +53,9 @@
+--- lib/iolib.h.orig	1993-02-09 16:35:27 UTC
++++ lib/iolib.h
+@@ -53,9 +53,9 @@ sprintf() can spew out some very large strings of char
  conditions. Assume its really only one (or maybe 2-3) lines. ps_ is similar, 
  but for internal use only by the functions in this library.
  
@@ -12,7 +12,7 @@
  However, the string space used to hold the input line is reused, and
  any pointers into the ln string which you saved may point to trash
  after one of these calls. Ln is alloced for 2K chars, leaving lots of
-@@ -66,7 +66,7 @@
+@@ -66,7 +66,7 @@ processing on the output string, including trying to w
  word breaks, converting tabs to spaces (every 8 chars), buffering
  output (perhaps multiple lines!) and more. The do_fwrite() function does
  not do this. Similarly, the getln() function despace()es,
@@ -21,7 +21,7 @@
  finput() functions do not [yes, it's a somewhat odd inconsistancy, but
  it's handy].
  
-@@ -254,6 +254,14 @@
+@@ -254,6 +254,14 @@ bool string_editor(); /* args: char *prompt, *str; int
     files! (The obvious exception is logging and input redirection, for which
     you should use the rather carefuly crafted routines described above!) */
  
@@ -36,7 +36,7 @@
  bool make_filename(); /* args: char *name; int mode; char *extension; 
     This turns name into a perfectly valid file name, and returns TRUE if this
     was possible. The name may include a directory specification - otherwise it
-@@ -277,7 +285,7 @@
+@@ -277,7 +285,7 @@ FILE *open_file();  /* args: char *name, *mode; on fai
  #define APPEND "a"
  void close_file();  /* args: FILE *fp; */
  
@@ -45,7 +45,7 @@
     will be able to grab a new line from the file. */
  bool end_of_text(); /* args: FILE *fp; Like an end-of-file test, except it also
    returns TRUE if rest of the file is white. As a side-effect, it will step
-@@ -289,17 +297,17 @@
+@@ -289,17 +297,17 @@ void do_fwrite(); /* args: FILE *fp; char *string; no 
  
  #define fpr(fp) fprint(fp,ps)
  #define fwp(fp) fwrite(fp,ps)
@@ -67,7 +67,7 @@
     beginning with a '#' in the leftmost position. Also, each time any line is
     read from the file (data, null, or comment), *count is incremented. */
  		     
-@@ -329,7 +337,7 @@
+@@ -329,7 +337,7 @@ extern int num_file_args, dos_output, prep_it, append_
  
  extern char *ps_, *ln_;     /* input and output strings for the library only */
  extern char *linebuf;       /* tty output buffer */
diff --git a/biology/mapm3/files/patch-lib-makehelp.c b/biology/mapm3/files/patch-lib-makehelp.c
index b32c1600d4d1..831d8d23ce72 100644
--- a/biology/mapm3/files/patch-lib-makehelp.c
+++ b/biology/mapm3/files/patch-lib-makehelp.c
@@ -1,6 +1,6 @@
---- lib/makehelp.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/makehelp.c	2008-03-27 21:52:37.000000000 +0000
-@@ -131,7 +131,7 @@
+--- lib/makehelp.c.orig	1993-02-09 21:19:35 UTC
++++ lib/makehelp.c
+@@ -131,7 +131,7 @@ char *name;
  {
      close_file(file);
  
@@ -9,7 +9,7 @@
      close_file(hlp);
  
      write_topics_and_end();
-@@ -172,9 +172,9 @@
+@@ -172,9 +172,9 @@ char *argv[];
  	strcpy(man_name, argv[4]);
  
  	strcpy(code_failed,code_name);
@@ -21,7 +21,7 @@
  			     FORCE_DIR,argv[5]);
  
  	file= open_file(file_name,READ);
-@@ -187,16 +187,16 @@
+@@ -187,16 +187,16 @@ char *argv[];
  	matrix(entry,MAX_COMMANDS,MAXLINE+1,char);
  
  	/* start help file 12345678901234567890123456789012345 */
@@ -43,7 +43,7 @@
  
  	/* man file */
  	man_write_title();
-@@ -242,7 +242,7 @@
+@@ -242,7 +242,7 @@ char *argv[];
  	    strcpy(name,str+i); despace(name);
  	    nextstr();
  	    sf(ps,"\t%s...  ",name); pr(); flush();
@@ -52,7 +52,7 @@
  	    if      (streq(type,"cmd"))   parse_entry(CMD,name,abbreviation); 
  	    else if (streq(type,"opt"))   parse_entry(OPT,name,abbreviation); 
  	    else if (streq(type,"param")) parse_entry(PAR,name,abbreviation);
-@@ -419,7 +419,7 @@
+@@ -419,7 +419,7 @@ void write_topics_and_end()
  	sf(ps," mktopic(%d,\"%s\",TOP,%ldl);\n",s,temp,position[s]);
  	fpr(code); s++;
      }
@@ -61,7 +61,7 @@
  }
  
  
-@@ -681,7 +681,7 @@
+@@ -681,7 +681,7 @@ void man_write_contents()
  	    case TOP:
  	      man_write_line("");
  	      strcpy(upcase,section[s]); uppercase(upcase);
@@ -70,7 +70,7 @@
  	    case CMD: 
  	      strcpy(upcase,entry[i]); uppercase(upcase);
  	      sf(temp,"      %s Command ",upcase); break;
-@@ -718,7 +718,7 @@
+@@ -718,7 +718,7 @@ void man_write_contents()
  	if (entry_type[i]==TOP) {
  	    man_write_line("");
  	    strcpy(upcase,section[s]); uppercase(upcase);
diff --git a/biology/mapm3/files/patch-lib-shell.c b/biology/mapm3/files/patch-lib-shell.c
index b558288fd6aa..6f7f6d3027f3 100644
--- a/biology/mapm3/files/patch-lib-shell.c
+++ b/biology/mapm3/files/patch-lib-shell.c
@@ -1,6 +1,6 @@
---- lib/shell.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/shell.c	2008-03-27 21:24:20.000000000 +0000
-@@ -129,7 +129,7 @@
+--- lib/shell.c.orig	1993-02-09 16:35:25 UTC
++++ lib/shell.c
+@@ -129,7 +129,7 @@ char *version_filename;
  
      run {
  	strcpy(name,version_filename);
@@ -9,7 +9,7 @@
  				  FORCE_DIR,CODE_DIR)) send(CANTOPEN); 
  	fp=open_file(name,READ);
  	finput(fp,ln_,MAXLINE); p=ln_; /* don't hack &ln_ */
-@@ -226,7 +226,7 @@
+@@ -226,7 +226,7 @@ char *program, *version, *copyright, *help_filename; 
      help_uses_wimp_help=  FALSE;
  
      help_file=NULL;
@@ -18,7 +18,7 @@
  			     DEFAULT_DIR,CODE_DIR)) {
  	run help_file=open_file(help_filename,READ);
  	  except_when(CANTOPEN) {}
-@@ -950,7 +950,7 @@
+@@ -950,7 +950,7 @@ command run_from_file()
      use_uncrunched_args();
      get_one_arg(stoken,sREQUIRED,file_name);
  
@@ -27,7 +27,7 @@
        error("bad input file name");
      else redirect_input(file_name,TRUE); /* verbose -> messages */
  }
-@@ -972,7 +972,7 @@
+@@ -972,7 +972,7 @@ command do_photo()
  	usage_error(1);
  
      } else if (!nullstr(file_name)) {
@@ -36,7 +36,7 @@
  	  sf(ps,"error: Bad photo file name");
  	if (!photo_to_file(file_name,"a")) 
  	  sf(ps,"error: Unable to open photo file '%s'\n",file_name); 
-@@ -1080,12 +1080,12 @@
+@@ -1080,12 +1080,12 @@ command help()
  		else if (topic_help_key[i]==HELPLESS) print(NO_HELP_KEY);
  		else {
  		    fgoto_line(help_file,topic_help_key[i]);
@@ -51,7 +51,7 @@
  		    }
  		    if (!got_any) print(NO_HELP_KEY);
  		}
-@@ -1131,12 +1131,12 @@
+@@ -1131,12 +1131,12 @@ command help()
  		else if (cmd[i]->help_key==HELPLESS) print(NO_HELP_KEY);
  		else {
  		    fgoto_line(help_file,cmd[i]->help_key);
@@ -66,7 +66,7 @@
  		    }
  		    if (!got_any) print(NO_HELP_KEY);
  		}
-@@ -1164,10 +1164,10 @@
+@@ -1164,10 +1164,10 @@ command about()
        { print(NO_HELP_KEY); nl(); print(SURROGATE_ABOUT); }
      else {
  	fgoto_line(help_file,n);
diff --git a/biology/mapm3/files/patch-lib-syscode.c b/biology/mapm3/files/patch-lib-syscode.c
index c74d4b58c6ce..5abb6ffcc954 100644
--- a/biology/mapm3/files/patch-lib-syscode.c
+++ b/biology/mapm3/files/patch-lib-syscode.c
@@ -1,6 +1,6 @@
---- lib/syscode.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/syscode.c	2008-03-27 21:03:12.000000000 +0000
-@@ -198,7 +198,7 @@
+--- lib/syscode.c.orig	1993-02-09 16:35:26 UTC
++++ lib/syscode.c
+@@ -198,7 +198,7 @@ long index;
      long fseekvalue= 0L;
      frewind(fp);
      run while (fseekvalue < index-1) {
@@ -9,7 +9,7 @@
  	fseekvalue+=len(ln)+1;
      } except_when(ENDOFILE) return(FALSE);
      return(TRUE);
-@@ -742,26 +742,26 @@
+@@ -742,26 +742,26 @@ char *argv[];
  
  	} else if (matches(argv[i]+1,"load")) {
  	    check_file_arg(*argc_ptr-i,argv[i+1],file_arg[LOAD_FILE_ARG],
diff --git a/biology/mapm3/files/patch-lib-system.h b/biology/mapm3/files/patch-lib-system.h
index a030b5a46fd2..76b5289a231d 100644
--- a/biology/mapm3/files/patch-lib-system.h
+++ b/biology/mapm3/files/patch-lib-system.h
@@ -1,6 +1,6 @@
---- lib/system.h.orig	2008-04-04 20:05:29.000000000 +0000
-+++ lib/system.h	2008-03-27 20:49:34.000000000 +0000
-@@ -43,6 +43,7 @@
+--- lib/system.h.orig	1993-02-09 16:35:28 UTC
++++ lib/system.h
+@@ -43,6 +43,7 @@ code, we suggest you use the following flags:
     _SYS_OSF	Specifics for OSF/1 for DEC Alpha (like, if it ever ships)
     _SYS_AIX	Specifics for the inferior but marketable AIX (RISC or other?)
     _SYS_HPUX	Specifics for HP-UX (8.x?) for HP 9000/700 series.
@@ -8,7 +8,7 @@
     _SYS_UNIX	Basic Unix semantics, defined if any one of the above is
  
     _SYS_WATCOM  Specifics for WATCOM C/386 9.0 with apropriate libraries
-@@ -86,6 +87,11 @@
+@@ -86,9 +87,14 @@ following and then #including "system.h":
  #else
  #ifdef  _SYS_AUX
  #define _SYS_UNIX  /* Note: NOT _SYS_MAC */
@@ -16,11 +16,14 @@
 +#ifdef  _SYS_BSD
 +#define _SYS_UNIX
 +#else
-+#endif
  #endif
  #endif
  #endif
-@@ -191,6 +197,9 @@
++#endif
+ #ifdef _SYS_WATCOM
+ #define _SYS_DOS
+ #endif
+@@ -191,6 +197,9 @@ extern char *sys_errlist[]; extern int sys_nerr;
  #ifdef _SYS_ULTRIX
  #define SIGHANDLE void
  #endif
@@ -30,7 +33,7 @@
  
  
  
-@@ -210,10 +219,14 @@
+@@ -210,10 +219,14 @@ seem to be real portable, so be careful.
  #ifdef _SYS_ULTRIX
  #define USE_RANDOM
  #else
@@ -45,7 +48,7 @@
  
  
  /***************************** C-Library **************************************
-@@ -282,6 +295,14 @@
+@@ -282,6 +295,14 @@ Check out their usage (arguments, etc) in syscode.c to
  #define QSORT_LENGTH       int   /* actually width is an int, not a unsigned */
  #endif
  
@@ -60,7 +63,7 @@
  #ifdef _SYS_AUX     /* just like ULTRIX? */
  #define CALLOC_PTR_TO      char
  #define CALLOC_NUM_TYPE	   size_t /* unsigned in man page is wrong? */
-@@ -583,7 +604,7 @@
+@@ -583,7 +604,7 @@ robust and portable) interfaces are provided by the li
  #include <signal.h> 
  #include <errno.h> 	
  #include <time.h>       /* for ctime() def - Who does not have this file? */
diff --git a/biology/mapm3/files/patch-mapm-chroms.c b/biology/mapm3/files/patch-mapm-chroms.c
index c05d3afac62e..80036ce76dee 100644
--- a/biology/mapm3/files/patch-mapm-chroms.c
+++ b/biology/mapm3/files/patch-mapm-chroms.c
@@ -1,6 +1,6 @@
---- mapm/chroms.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/chroms.c	2008-03-27 21:25:42.000000000 +0000
-@@ -909,7 +909,7 @@
+--- mapm/chroms.c.orig	1993-02-09 16:35:02 UTC
++++ mapm/chroms.c
+@@ -909,7 +909,7 @@ FILE *fp;
          write_map(fp, chromosome->map_list[i]);
      }
     
@@ -9,7 +9,7 @@
      for (locus=0; locus< raw.num_markers; locus++) {
          sf(ps,"*%-8s %2d",raw.locus_name[locus],assignment[locus]->status); 
  	fpr(fp);
-@@ -943,7 +943,7 @@
+@@ -943,7 +943,7 @@ FILE *fp;
      MAP  *map;
  
      /* chromosomes */
@@ -18,7 +18,7 @@
      stoken(&ln,sREQUIRED,word);
      if (!streq(word,"*Chromosomes:") || !itoken(&ln,iREQUIRED,&num_chroms)) {
          baddata("error finding *Chromosomes:");
-@@ -957,7 +957,7 @@
+@@ -957,7 +957,7 @@ FILE *fp;
          baddata("listed number of chromosomes and actual number do not agree");
      }
  
diff --git a/biology/mapm3/files/patch-mapm-database.c b/biology/mapm3/files/patch-mapm-database.c
index bed345d6f69a..b8c49a5fa58c 100644
--- a/biology/mapm3/files/patch-mapm-database.c
+++ b/biology/mapm3/files/patch-mapm-database.c
@@ -1,6 +1,6 @@
---- mapm/database.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/database.c	2008-03-27 21:26:48.000000000 +0000
-@@ -45,7 +45,7 @@
+--- mapm/database.c.orig	1993-02-09 16:35:02 UTC
++++ mapm/database.c
+@@ -45,7 +45,7 @@ command import()
      get_one_arg(stoken, sREQUIRED, out_name);
  
      /* force file extension to be ".data" */
diff --git a/biology/mapm3/files/patch-mapm-info.c b/biology/mapm3/files/patch-mapm-info.c
index d90cc8cb2a38..6aaccbac6d06 100644
--- a/biology/mapm3/files/patch-mapm-info.c
+++ b/biology/mapm3/files/patch-mapm-info.c
@@ -1,6 +1,6 @@
---- mapm/info.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/info.c	2008-03-27 21:26:18.000000000 +0000
-@@ -966,9 +966,9 @@
+--- mapm/info.c.orig	1993-02-09 16:35:03 UTC
++++ mapm/info.c
+@@ -966,9 +966,9 @@ FILE *fp;
  	   class[locus]);
  	fpr(fp);
      }
@@ -12,7 +12,7 @@
  }
  
  
-@@ -980,12 +980,12 @@
+@@ -980,12 +980,12 @@ FILE *fp;
      real rate;
      char temp_locus_name[NAME_LEN+2], word[TOKLEN+1];
  
@@ -27,7 +27,7 @@
  
  	if (!nstoken(&ln,sREQUIRED,temp_locus_name,NAME_LEN+1) || 
  	    temp_locus_name[0]!='*' || len(temp_locus_name)<2)
-@@ -1007,9 +1007,9 @@
+@@ -1007,9 +1007,9 @@ FILE *fp;
  	order_next[locus]= ord_next;
  	class[locus]= class_num;
      }
diff --git a/biology/mapm3/files/patch-mapm-map_info.h b/biology/mapm3/files/patch-mapm-map_info.h
index d16778b5dc62..c965651d3de9 100644
--- a/biology/mapm3/files/patch-mapm-map_info.h
+++ b/biology/mapm3/files/patch-mapm-map_info.h
@@ -1,6 +1,6 @@
---- mapm/map_info.h.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/map_info.h	2008-03-31 00:14:48.000000000 +0000
-@@ -215,7 +215,7 @@
+--- mapm/map_info.h.orig	1993-02-09 16:35:06 UTC
++++ mapm/map_info.h
+@@ -215,7 +215,7 @@ typedef struct {  /* working data for place cmd and ex
  /***** Chromosome framework, assignment, and placement stuff - chroms.c *****/
  
  extern SAVED_LIST *chromosome;  /* malloced by allocate_mapping_structs() */
diff --git a/biology/mapm3/files/patch-mapm-mapm.h b/biology/mapm3/files/patch-mapm-mapm.h
index 95473a631fa7..f4495596b999 100644
--- a/biology/mapm3/files/patch-mapm-mapm.h
+++ b/biology/mapm3/files/patch-mapm-mapm.h
@@ -1,5 +1,5 @@
---- mapm/mapm.h.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/mapm.h	2008-03-16 13:53:32.000000000 +0000
+--- mapm/mapm.h.orig	1993-02-09 16:35:06 UTC
++++ mapm/mapm.h
 @@ -19,7 +19,7 @@
  #define command void /* needed if INC_SHELL was not defined */
  #endif
diff --git a/biology/mapm3/files/patch-mapm-maps.c b/biology/mapm3/files/patch-mapm-maps.c
index 7fa271809f84..9bb07ce56ab2 100644
--- a/biology/mapm3/files/patch-mapm-maps.c
+++ b/biology/mapm3/files/patch-mapm-maps.c
@@ -1,6 +1,6 @@
---- mapm/maps.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/maps.c	2008-03-23 15:39:56.000000000 +0000
-@@ -592,7 +592,7 @@
+--- mapm/maps.c.orig	1993-02-09 16:35:03 UTC
++++ mapm/maps.c
+@@ -592,7 +592,7 @@ MAP *map;
   
      clean_map(map);
      
@@ -9,7 +9,7 @@
      if (!nstoken(&ln,sREQUIRED,name,NAME_LEN+1) || name[0]!='*' ||
  	sscanf(ln,"%d %d %d %d %lf",&num_loci,&unlink,&sex,&errors,&like)!=5)
        baddata("expected *chrom-name # # # #");
-@@ -603,31 +603,31 @@
+@@ -603,31 +603,31 @@ MAP *map;
      strcpy(map->map_name,name+1); map->allow_errors= errors;
      map->num_loci=num_loci;       map->log_like=like;
  
@@ -49,7 +49,7 @@
  	if (!itoken(&ln,iREQUIRED,&num)) send(CRASH);
  	map->fix_interval[i]=num;
      }   
-@@ -637,7 +637,7 @@
+@@ -637,7 +637,7 @@ MAP *map;
  	    matrix(map->error_lod,map->max_loci,raw.data.f2.num_indivs,real);
  	}
  	for (i=0; i<map->num_loci; i++) {
@@ -58,7 +58,7 @@
  	    if (!stoken(&ln,sREQUIRED,str) || !streq(str,"errors")) 
  	      send(CRASH);
  	    if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
-@@ -646,9 +646,9 @@
+@@ -646,9 +646,9 @@ MAP *map;
  		for(j=0; j<raw.data.f2.num_indivs; j++) 
  		  map->error_lod[i][j]= 0.0;
  	    } else {
diff --git a/biology/mapm3/files/patch-mapm-npt_cmds.c b/biology/mapm3/files/patch-mapm-npt_cmds.c
index 7eb33051e6c6..796ad00c5471 100644
--- a/biology/mapm3/files/patch-mapm-npt_cmds.c
+++ b/biology/mapm3/files/patch-mapm-npt_cmds.c
@@ -1,6 +1,6 @@
---- mapm/npt_cmds.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/npt_cmds.c	2008-03-27 21:27:12.000000000 +0000
-@@ -78,7 +78,7 @@
+--- mapm/npt_cmds.c.orig	1993-02-09 16:35:04 UTC
++++ mapm/npt_cmds.c
+@@ -78,7 +78,7 @@ command draw_map()
      nomore_args(num_args);
  
      run {
diff --git a/biology/mapm3/files/patch-mapm-print.c b/biology/mapm3/files/patch-mapm-print.c
index 02cdedf67133..fcf34f3e5c5b 100644
--- a/biology/mapm3/files/patch-mapm-print.c
+++ b/biology/mapm3/files/patch-mapm-print.c
@@ -1,6 +1,6 @@
---- mapm/print.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/print.c	2008-03-27 21:34:40.000000000 +0000
-@@ -540,7 +540,7 @@
+--- mapm/print.c.orig	1993-02-09 16:35:04 UTC
++++ mapm/print.c
+@@ -540,7 +540,7 @@ bool haplo;
      }    
  }
  
diff --git a/biology/mapm3/files/patch-mapm-reader.c b/biology/mapm3/files/patch-mapm-reader.c
index d6e122742099..994dee525874 100644
--- a/biology/mapm3/files/patch-mapm-reader.c
+++ b/biology/mapm3/files/patch-mapm-reader.c
@@ -1,6 +1,6 @@
---- mapm/reader.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/reader.c	2008-03-27 21:10:18.000000000 +0000
-@@ -81,7 +81,7 @@
+--- mapm/reader.c.orig	1993-02-09 16:35:05 UTC
++++ mapm/reader.c
+@@ -81,7 +81,7 @@ void data_init()
  
  void getdataln(fp) /* get next nonblank,noncomment data file line */
  FILE *fp;
@@ -9,7 +9,7 @@
  
    
  void baddata(reason) /* send data reading error message */
-@@ -135,7 +135,7 @@
+@@ -135,7 +135,7 @@ bool *exists;
      char tmpname[PATH_LENGTH+1];
  
      make_filename(name,FORCE_EXTENSION,ext);
@@ -18,7 +18,7 @@
     
      fp=NULL; *exists=FALSE;
      run {
-@@ -162,7 +162,7 @@
+@@ -162,7 +162,7 @@ char *name, *oldext;
  bool exists;
  {
      char tmpname[PATH_LENGTH+1], oldname[PATH_LENGTH+1];
@@ -27,7 +27,7 @@
      strcpy(oldname,name); make_filename(oldname,FORCE_EXTENSION,oldext);
  
      if (exists) { rename_file(name,oldname); }
-@@ -214,7 +214,7 @@
+@@ -214,7 +214,7 @@ bool israw;
  		raw.data.f2.cross_type);
      print(" ok\n");
  
@@ -36,7 +36,7 @@
      run {
  	fp2=NULL;
          fp2=open_file(name,READ);
-@@ -228,7 +228,7 @@
+@@ -228,7 +228,7 @@ bool israw;
  	close_file(fp2);
      } except_when(CANTOPEN) { } /* need a better handler */
  
@@ -45,7 +45,7 @@
      run {
  	fp2=NULL;
  	fp2=open_file(name,READ);
-@@ -240,7 +240,7 @@
+@@ -240,7 +240,7 @@ bool israw;
  	close_file(fp2);
      } except_when(CANTOPEN) { } /* need a better handler */
  
@@ -54,7 +54,7 @@
      run {
  	fp2=NULL;
          fp2=open_file(name,READ);
-@@ -285,39 +285,39 @@
+@@ -285,39 +285,39 @@ bool save_genos_too;
      run {
  	strcpy(name,base_name);
  	if (save_genos_too) {
@@ -104,7 +104,7 @@
  	    free_traits();
  	}
  	two_pt_touched= FALSE;
-@@ -576,15 +576,15 @@
+@@ -576,15 +576,15 @@ FILE *fp;
      char header[MAXLINE+1];
  
      if (raw.data.f2.cross_type==F2_INTERCROSS) 
@@ -125,7 +125,7 @@
      
      sf(header,"%d %d %d\n",raw.filenumber,raw.data.f2.num_indivs,
         raw.num_markers); fprint(fp,header);
-@@ -593,7 +593,7 @@
+@@ -593,7 +593,7 @@ FILE *fp;
  	sf(ps,"*%-10s   ", raw.locus_name[i]);
  	fpr(fp);
  	for (j=0; j<raw.data.f2.num_indivs; j++) {
@@ -134,7 +134,7 @@
  	    sf(ps,"%c",raw.data.f2.allele[i][j]);
  	    fpr(fp);
  	    }
-@@ -828,9 +828,7 @@
+@@ -828,9 +828,7 @@ int chr;
  char *symb;
  {
      /* CHANGED FOR THIS VERION - NOW READS "-AHBCD" */
@@ -145,7 +145,7 @@
      else if (chr==symb[2]) return(HYBRID_TYPE_H);
      else if (chr==symb[3]) return(PARENTAL_TYPE_B);
      else if (chr==symb[4]) return(TYPE_NOT_A);
-@@ -856,26 +854,26 @@
+@@ -856,26 +854,26 @@ FILE *fp;
  	fnl(fp);
      }
      fnl(fp);
diff --git a/biology/mapm3/files/patch-mapm-state.c b/biology/mapm3/files/patch-mapm-state.c
index b27e385af297..612e8b858bdd 100644
--- a/biology/mapm3/files/patch-mapm-state.c
+++ b/biology/mapm3/files/patch-mapm-state.c
@@ -1,6 +1,6 @@
---- mapm/state.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/state.c	2008-04-03 19:37:40.000000000 +0000
-@@ -734,7 +734,7 @@
+--- mapm/state.c.orig	1993-02-09 16:35:05 UTC
++++ mapm/state.c
+@@ -734,7 +734,7 @@ FILE *fp;
  {
      int i, usenum;
  
@@ -9,7 +9,7 @@
  
      sf(ps,"*PrintNames: %d\n",print_names); fpr(fp);
      sf(ps,"*Tolerance: %lf\n",tolerance); fpr(fp);
-@@ -852,5 +852,5 @@
+@@ -852,5 +852,5 @@ FILE *fp;
  	load_table(context[i]->sequence_history,fp,INDEX_BY_NUMBER,num);
      }
  
diff --git a/biology/mapm3/files/patch-mapm-sys_cmds.c b/biology/mapm3/files/patch-mapm-sys_cmds.c
index 9307cf7feb6e..0cbb7a480765 100644
--- a/biology/mapm3/files/patch-mapm-sys_cmds.c
+++ b/biology/mapm3/files/patch-mapm-sys_cmds.c
@@ -1,6 +1,6 @@
---- mapm/sys_cmds.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/sys_cmds.c	2008-03-27 21:28:05.000000000 +0000
-@@ -98,7 +98,7 @@
+--- mapm/sys_cmds.c.orig	1993-02-09 16:35:06 UTC
++++ mapm/sys_cmds.c
+@@ -98,7 +98,7 @@ bool prev_data, raw;
  	close_file(fp);
  	if (raw) {
  	    strcpy(run_file,name); 
@@ -9,7 +9,7 @@
  	    if (!redirect_input(run_file,FALSE)) {
  		sf(ps,"unable to run file '%s'... skipping initialization\n",
  		   run_file); pr();
-@@ -145,7 +145,7 @@
+@@ -145,7 +145,7 @@ command new_load_data()
  	if (!prev_data) print("no data are loaded\n");
  	else { sf(ps,DATA_LOADED,raw.filename,data_info(TRUE)); pr(); }
      } else {
@@ -18,7 +18,7 @@
  	if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared);
  	try_to_load(fp,name,prev_data,FALSE);
  	just_prepared=FALSE;
-@@ -169,7 +169,7 @@
+@@ -169,7 +169,7 @@ command new_prepare()
         if (streq(&name[end-4],DATA_EXT) || streq(&name[end-4],DATA_OLD) ||...
         error(RAW_EXTENSION); */
  
@@ -27,7 +27,7 @@
      if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared);
      try_to_load(fp,name,prev_data,TRUE);
      just_prepared=TRUE;
-@@ -186,7 +186,7 @@
+@@ -186,7 +186,7 @@ command new_save_data()
      get_one_arg(stoken,"",name); new_name= !nullstr(name);
      /* want to change this so it sets raw.filename only AFTER it writes OK */
  
@@ -36,7 +36,7 @@
        { sf(ps,BAD_FILENAME,name); error(ps); }
  
      run {
-@@ -621,7 +621,7 @@
+@@ -621,7 +621,7 @@ command new_insert()
  	for (j=num_seq_tokens-1; j>i; j--)
  	  strcpy(seq_tokens[j+1],seq_tokens[j]);
  	/* this is severly broken, if len(appendage) > TOKLEN */
diff --git a/biology/mapm3/files/patch-mapm-two_cmds.c b/biology/mapm3/files/patch-mapm-two_cmds.c
index bfb068015135..fe1e3eebf760 100644
--- a/biology/mapm3/files/patch-mapm-two_cmds.c
+++ b/biology/mapm3/files/patch-mapm-two_cmds.c
@@ -1,6 +1,6 @@
---- mapm/two_cmds.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ mapm/two_cmds.c	2008-04-03 19:58:42.000000000 +0000
-@@ -698,11 +698,11 @@
+--- mapm/two_cmds.c.orig	1993-02-09 16:35:06 UTC
++++ mapm/two_cmds.c
+@@ -698,11 +698,11 @@ command three_point()
  
  	if (!print_names) {
  print("\n                    log-likelihood differences\n");
diff --git a/biology/mapm3/files/patch-quant-qcmds.c b/biology/mapm3/files/patch-quant-qcmds.c
index 39bee743f5d4..4cb24178d03e 100644
--- a/biology/mapm3/files/patch-quant-qcmds.c
+++ b/biology/mapm3/files/patch-quant-qcmds.c
@@ -1,6 +1,6 @@
---- quant/qcmds.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ quant/qcmds.c	2008-03-27 21:30:08.000000000 +0000
-@@ -1348,7 +1348,7 @@
+--- quant/qcmds.c.orig	1993-02-09 21:12:33 UTC
++++ quant/qcmds.c
+@@ -1348,7 +1348,7 @@ command load_data() 
      if (nullstr(args)) {
  	if (!data_loaded()) print(NO_LOADED_DATA); else {
  	    strcpy(tfile,raw.file);
@@ -9,7 +9,7 @@
  	    sf(ps,LOADED_DATA,raw.file,tfile,"",raw.n_indivs,
  	       (raw.data_type==BACKCROSS ? "backcross":"intercross"),
  	       raw.n_loci,raw.n_traits,maybe_s(raw.n_traits)); pr();
-@@ -1363,9 +1363,9 @@
+@@ -1363,9 +1363,9 @@ command load_data() 
  	nstoken(&args,sREQUIRED,dfile,PATH_LENGTH); tfile[0]='\0';
  	nomore_args(num_args);
  	run {
@@ -21,7 +21,7 @@
  
  	    if (streq(ln,"prepared data f2 backcross")) {
  		strcpy(geno_chars,default_backcross_chars);
-@@ -1384,11 +1384,11 @@
+@@ -1384,11 +1384,11 @@ command load_data() 
  	    }
  
  	    strcpy(tfile,dfile);
@@ -35,7 +35,7 @@
  	      send(CANTOPEN);
  	    fpc = open_file(mfile,READ);
  
-@@ -1449,7 +1449,7 @@
+@@ -1449,7 +1449,7 @@ command prep_data()
  
  	out_name = get_temp_string();
  	strcpy(out_name,in_name);
@@ -44,7 +44,7 @@
  
   fp = open_file(in_name,READ);
  	getdataln(fp);  crunch(ln);
-@@ -1488,7 +1488,7 @@
+@@ -1488,7 +1488,7 @@ command save_status()
      name = mkstrcpy(raw.file);
      name3 = mkstrcpy(raw.file);
      name2 = "dummy.qtls";
@@ -53,7 +53,7 @@
  
      /* The following accounts for the case where there is no file 'name'
         (i.e. it makes one)  */
-@@ -1500,7 +1500,7 @@
+@@ -1500,7 +1500,7 @@ command save_status()
  	close_file(fp);
      }
  
@@ -62,7 +62,7 @@
      run {
  	fp = open_file(name2, WRITE);
  	sf(ps,"Now saving %s...\n",name);  pr();
-@@ -1520,8 +1520,8 @@
+@@ -1520,8 +1520,8 @@ command save_status()
      }
  
      name2="dummy.traits";
@@ -73,7 +73,7 @@
      run {
  	fp = open_file(name2, WRITE);
  	sf(ps,"Now saving %s...\n",name);  pr();
-@@ -1560,7 +1560,7 @@
+@@ -1560,7 +1560,7 @@ FILE *fp;
  	save_wiggle(fp,i);
      }
      
@@ -82,7 +82,7 @@
      
      fprintf(fp,"%d %d\n",num_compares,first_compare);
      for(i = 0; i < num_compares; i++) {
-@@ -1587,7 +1587,7 @@
+@@ -1587,7 +1587,7 @@ void load_qtl_files()
  
      run {
  	strcpy(name,raw.file);
diff --git a/biology/mapm3/files/patch-quant-qraw.c b/biology/mapm3/files/patch-quant-qraw.c
index 5185a1c8c018..34f8ed7bb326 100644
--- a/biology/mapm3/files/patch-quant-qraw.c
+++ b/biology/mapm3/files/patch-quant-qraw.c
@@ -1,6 +1,6 @@
---- quant/qraw.c.orig	2008-04-04 20:05:29.000000000 +0000
-+++ quant/qraw.c	2008-03-27 21:30:39.000000000 +0000
-@@ -124,7 +124,7 @@
+--- quant/qraw.c.orig	1993-02-09 16:35:59 UTC
++++ quant/qraw.c
+@@ -124,7 +124,7 @@ int data_loaded() { return(raw.file[0]!='\0'); }
  
  void getdataln(fp) /* get next nonblank/noncomment data file line */
  FILE *fp;
@@ -9,7 +9,7 @@
    BADDATA_ln= ln; }
  real read_map_distance();
  void read_map_locus();
-@@ -426,13 +426,13 @@
+@@ -426,13 +426,13 @@ FILE *fp;
  
  	    for(j=0;j<raw.n_indivs;j++) {
  		if(j % 5 == 0 && j != 0)
@@ -25,7 +25,7 @@
  	sf(ps,"*Print mapm loci: %d\n", print_mapm_loci);fpr(fp);
  	sf(ps,"*Like tolerance: %lf\n",like_tolerance);fpr(fp);
  	sf(ps,"*Brute force: %d\n",brute_force);fpr(fp);
-@@ -452,21 +452,21 @@
+@@ -452,21 +452,21 @@ FILE *fp;
  	    sf(ps, "chr%d %d\n", i+1, raw.chrom_n_loci[i]); fpr(fp);
  	    for(j=0;j<raw.chrom_n_loci[i];j++) {
  		if(j % 18 == 0 && j != 0)
diff --git a/biology/mapm3/files/patch-sun-xmapmaker b/biology/mapm3/files/patch-sun-xmapmaker
index 03b5254505cf..f3177a127b51 100644
--- a/biology/mapm3/files/patch-sun-xmapmaker
+++ b/biology/mapm3/files/patch-sun-xmapmaker
@@ -1,6 +1,6 @@
---- sun/xmapmaker.orig	2008-04-04 20:05:29.000000000 +0000
-+++ sun/xmapmaker	2008-04-04 19:59:32.000000000 +0000
-@@ -10,5 +10,5 @@
+--- sun/xmapmaker.orig	1993-02-10 05:57:29 UTC
++++ sun/xmapmaker
+@@ -10,5 +10,5 @@ if (-e /usr/openwin/bin/xterm) then
  else if (-e /usr/openwin/demo/xterm) then
  	exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $*
  else
diff --git a/biology/mapm3/files/patch-sun-xqtl b/biology/mapm3/files/patch-sun-xqtl
index 963adade779f..f25537dcdf70 100644
--- a/biology/mapm3/files/patch-sun-xqtl
+++ b/biology/mapm3/files/patch-sun-xqtl
@@ -1,6 +1,6 @@
---- sun/xqtl.orig	2008-04-04 20:05:29.000000000 +0000
-+++ sun/xqtl	2008-04-04 19:59:41.000000000 +0000
-@@ -10,5 +10,5 @@
+--- sun/xqtl.orig	1993-02-10 05:57:29 UTC
++++ sun/xqtl
+@@ -10,5 +10,5 @@ if (-e /usr/openwin/bin/xterm) then
  else if (-e /usr/openwin/demo/xterm) then
  	exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $*
  else