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--- recombine.c.orig 2019-08-03 09:14:33 UTC |
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+++ recombine.c |
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@@ -169,7 +169,7 @@ void openfile(FILE **fp, char *filename, |
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file[0] = '\0'; |
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while (file[0] =='\0'){ |
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fprintf(stdout,"Please enter a new filename>"); |
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- gets(file); |
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+ fgets(file,100,stdin); |
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} |
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break; |
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case 'w': |
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@@ -177,7 +177,7 @@ void openfile(FILE **fp, char *filename, |
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file[0] = '\0'; |
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while (file[0] =='\0'){ |
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fprintf(stdout,"Please enter a new filename>"); |
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- gets(file); |
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+ fgets(file,100,stdin); |
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} |
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break; |
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} |
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@@ -1864,28 +1864,28 @@ if (strchr("#FLAHONESPGUMVRTD",ch) != NU |
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case 'R': |
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do { |
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printf("Relative mutation rate of trait?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->mutrait = atof(input); |
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} while (op->mutrait <= 0.0); |
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break; |
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case 'T': |
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do { |
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printf("Ratio of forward to back trait mutation?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->traitratio = atof(input); |
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} while (op->traitratio <= 0.0); |
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break; |
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case 'D': |
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do { |
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printf("Frequency of trait?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->pd = atof(input); |
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} while (op->pd <= 0.0 || op->pd >= 1.0); |
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break; |
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case 'A': |
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do { |
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printf("Number of drops while resimulating (0-2)?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->hapdrop = atol(input); |
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} while (op->hapdrop != 0 && op->hapdrop != 1 && op->hapdrop != 2); |
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default: |
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@@ -1972,7 +1972,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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case 'T': |
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do { |
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printf("Transition/transversion ratio?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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locus_ttratio = atof(input); |
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if (locus_ttratio < 0.5) |
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printf("TTratio cannot be less than 0.5\n"); |
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@@ -1991,13 +1991,13 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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op->panel = !op->panel; |
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if (op->panel) { |
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printf("Number of populations?\n"); |
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- gets(input); |
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+ ; |
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*numpop = atol(input); |
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op->numpanel = (long *)calloc(*numpop,sizeof(long)); |
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for(i = 0; i < *numpop; i++) { |
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printf("Number of panel haplotypes for population"); |
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printf(" %ld?\n",i+1); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->numpanel[i] = atol(input); |
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} |
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} else |
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@@ -2012,7 +2012,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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if (op->ctgry) { |
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do { |
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printf("Number of categories ?"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->categs = atoi(input); |
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} while (op->categs < 1); |
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free(op->rate); |
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@@ -2091,7 +2091,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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if (!op->watt) { |
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do { |
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printf("Initial theta estimate?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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theta0 = atof(input); |
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} while (theta0 <= 0.0); |
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} |
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@@ -2099,7 +2099,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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case 'Z': |
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printf("What recombination rate?\n"); |
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do { |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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rec0 = atof(input); |
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if (rec0 < 0.0) |
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printf("recombination rate must be non-negative\n"); |
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@@ -2108,7 +2108,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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case 'S': |
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do { |
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printf("How many Short Chains?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->numchains[0] = atoi(input); |
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if (op->numchains[0] < 0) |
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printf("Must be non-negative\n"); |
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@@ -2118,7 +2118,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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done = FALSE; |
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while (!done) { |
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printf("How often to sample trees?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->increm[0] = atoi(input); |
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if (op->increm[0] > 0) done = TRUE; |
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else printf("Must be a positive integer\n"); |
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@@ -2128,7 +2128,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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done = FALSE; |
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while (!done) { |
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printf("How many short steps?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->steps[0] = atoi(input); |
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if (op->steps[0] > 0) done = TRUE; |
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else printf("Must be a positive integer\n"); |
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@@ -2137,7 +2137,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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case 'L': |
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do { |
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printf("How many Long Chains?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->numchains[1] = atoi(input); |
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if (op->numchains[1] < 1) |
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printf("Must be a positive integer\n"); |
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@@ -2147,7 +2147,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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done = FALSE; |
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while (!done) { |
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printf("How often to sample trees?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->increm[1] = atoi(input); |
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if (op->increm[1] > 0) done = TRUE; |
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else printf("Must be a positive integer\n"); |
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@@ -2157,7 +2157,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! |
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done = FALSE; |
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while (!done) { |
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printf("How many long steps?\n"); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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op->steps[1] = atoi(input); |
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if (op->steps[1] > 0) done = TRUE; |
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else printf("Must be a positive integer\n"); |
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@@ -2239,7 +2239,7 @@ do { |
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if (menu1) print_startmenu(op,writeout); |
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else {print_datamenu(op); print_searchmenu(op);} |
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print_menuend(); |
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- gets(input); |
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+ fgets(input,LINESIZE,stdin); |
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ch = toupper((int)input[0]); |
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done = (ch == 'Y'); |
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if (!done) { |