Attachment 206231 Details for Bug 238685 – svn-diff-recombine

[patch] svn-diff-recombine

svn-diff-recombine (text/plain), 7.12 KB, created by Walter Schwarzenfeld on 2019-08-03 09:19:28 UTC

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Creator: Walter Schwarzenfeld

Created: 2019-08-03 09:19:28 UTC

Size: 7.12 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 507940)
>+++ Makefile	(working copy)
>@@ -3,6 +3,7 @@
> 
> PORTNAME=	recombine
> PORTVERSION=	1.41
>+PORTREVISION=	1
> CATEGORIES=	biology
> MASTER_SITES=	http://evolution.gs.washington.edu/lamarc/recombine/
> DISTNAME=	${PORTNAME}${PORTVERSION}.src.doc
>Index: files/patch-recombine.c
>===================================================================
>--- files/patch-recombine.c	(nonexistent)
>+++ files/patch-recombine.c	(working copy)
>@@ -0,0 +1,168 @@
>+--- recombine.c.orig	2019-08-03 09:14:33 UTC
>++++ recombine.c
>+@@ -169,7 +169,7 @@ void openfile(FILE **fp, char *filename,
>+         file[0] = '\0';
>+         while (file[0] =='\0'){
>+           fprintf(stdout,"Please enter a new filename>");
>+-          gets(file);
>++          fgets(file,100,stdin);
>+           }
>+         break;
>+       case 'w':
>+@@ -177,7 +177,7 @@ void openfile(FILE **fp, char *filename,
>+         file[0] = '\0';
>+         while (file[0] =='\0'){
>+           fprintf(stdout,"Please enter a new filename>");
>+-          gets(file);
>++          fgets(file,100,stdin);
>+           }
>+         break;
>+       }
>+@@ -1864,28 +1864,28 @@ if (strchr("#FLAHONESPGUMVRTD",ch) != NU
>+       case 'R':
>+          do {
>+             printf("Relative mutation rate of trait?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->mutrait = atof(input);
>+          } while (op->mutrait <= 0.0);
>+          break;
>+       case 'T':
>+          do {
>+             printf("Ratio of forward to back trait mutation?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->traitratio = atof(input);
>+          } while (op->traitratio <= 0.0);
>+          break;
>+       case 'D':
>+          do {
>+             printf("Frequency of trait?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->pd = atof(input);
>+          } while (op->pd <= 0.0 || op->pd >= 1.0);
>+          break;
>+       case 'A':
>+          do {
>+             printf("Number of drops while resimulating (0-2)?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->hapdrop = atol(input);
>+          } while (op->hapdrop != 0 && op->hapdrop != 1 && op->hapdrop != 2); 
>+       default:
>+@@ -1972,7 +1972,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+       case 'T':
>+          do {
>+             printf("Transition/transversion ratio?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             locus_ttratio = atof(input);
>+             if (locus_ttratio < 0.5)
>+                printf("TTratio cannot be less than 0.5\n");
>+@@ -1991,13 +1991,13 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          op->panel = !op->panel;
>+          if (op->panel) {
>+             printf("Number of populations?\n");
>+-            gets(input);
>++            ;
>+             *numpop = atol(input);
>+             op->numpanel = (long *)calloc(*numpop,sizeof(long));
>+             for(i = 0; i < *numpop; i++) {
>+                printf("Number of panel haplotypes for population");
>+                printf(" %ld?\n",i+1);
>+-               gets(input);
>++               fgets(input,LINESIZE,stdin);
>+                op->numpanel[i] = atol(input);
>+             }
>+          } else
>+@@ -2012,7 +2012,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          if (op->ctgry) {
>+             do {
>+                printf("Number of categories ?");
>+-               gets(input);
>++               fgets(input,LINESIZE,stdin);
>+                op->categs = atoi(input);
>+             } while (op->categs < 1);
>+             free(op->rate);
>+@@ -2091,7 +2091,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          if (!op->watt) {
>+             do {
>+                printf("Initial theta estimate?\n");
>+-               gets(input);
>++               fgets(input,LINESIZE,stdin);
>+                theta0 = atof(input);
>+             } while (theta0 <= 0.0);
>+          }
>+@@ -2099,7 +2099,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+       case 'Z':
>+          printf("What recombination rate?\n");
>+          do {
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             rec0 = atof(input);
>+             if (rec0 < 0.0)
>+                printf("recombination rate must be non-negative\n");
>+@@ -2108,7 +2108,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+       case 'S':
>+          do {
>+             printf("How many Short Chains?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->numchains[0] = atoi(input);
>+             if (op->numchains[0] < 0)
>+             printf("Must be non-negative\n");
>+@@ -2118,7 +2118,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          done = FALSE;
>+          while (!done) {
>+             printf("How often to sample trees?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->increm[0] = atoi(input);
>+             if (op->increm[0] > 0) done = TRUE;
>+             else printf("Must be a positive integer\n");
>+@@ -2128,7 +2128,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          done = FALSE;
>+          while (!done) {
>+             printf("How many short steps?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->steps[0] = atoi(input);
>+             if (op->steps[0] > 0) done = TRUE;
>+             else printf("Must be a positive integer\n");
>+@@ -2137,7 +2137,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+       case 'L':
>+          do {
>+             printf("How many Long Chains?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->numchains[1] = atoi(input);
>+             if (op->numchains[1] < 1)
>+             printf("Must be a positive integer\n");
>+@@ -2147,7 +2147,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          done = FALSE;
>+          while (!done) {
>+             printf("How often to sample trees?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->increm[1] = atoi(input);
>+             if (op->increm[1] > 0) done = TRUE;
>+             else printf("Must be a positive integer\n");
>+@@ -2157,7 +2157,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) !
>+          done = FALSE;
>+          while (!done) {
>+             printf("How many long steps?\n");
>+-            gets(input);
>++            fgets(input,LINESIZE,stdin);
>+             op->steps[1] = atoi(input);
>+             if (op->steps[1] > 0) done = TRUE;
>+             else printf("Must be a positive integer\n");
>+@@ -2239,7 +2239,7 @@ do {
>+    if (menu1) print_startmenu(op,writeout);
>+    else {print_datamenu(op); print_searchmenu(op);}
>+    print_menuend();
>+-   gets(input);
>++   fgets(input,LINESIZE,stdin);
>+    ch = toupper((int)input[0]);
>+    done = (ch == 'Y');
>+    if (!done) {
>
>Property changes on: files/patch-recombine.c
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 238685: 206231