7e14529975
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
72 lines
2.1 KiB
C
72 lines
2.1 KiB
C
--- mapm/maps.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ mapm/maps.c 2008-03-23 15:39:56.000000000 +0000
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@@ -592,7 +592,7 @@
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clean_map(map);
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- fgetln(fp);
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+ fgetln_(fp);
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if (!nstoken(&ln,sREQUIRED,name,NAME_LEN+1) || name[0]!='*' ||
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sscanf(ln,"%d %d %d %d %lf",&num_loci,&unlink,&sex,&errors,&like)!=5)
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baddata("expected *chrom-name # # # #");
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@@ -603,31 +603,31 @@
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strcpy(map->map_name,name+1); map->allow_errors= errors;
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map->num_loci=num_loci; map->log_like=like;
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- fgetln(fp);
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+ fgetln_(fp);
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for (i=0; i<num_loci; i++) {
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- if (nullstr(ln)) fgetln(fp);
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+ if (nullstr(ln)) fgetln_(fp);
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if (!itoken(&ln,iREQUIRED,&num)) send(CRASH);
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map->locus[i]=num;
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}
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- fgetln(fp);
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+ fgetln_(fp);
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for (i=0; i<num_loci-1; i++) {
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- if (nullstr(ln)) fgetln(fp);
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+ if (nullstr(ln)) fgetln_(fp);
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if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
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map->rec_frac[i][MALE]=rnum;
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}
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if (raw.data_type==CEPH && sex) {
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- fgetln(fp);
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+ fgetln_(fp);
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for(i=0; i<num_loci-1; i++) {
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- if (nullstr(ln)) fgetln(fp);
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+ if (nullstr(ln)) fgetln_(fp);
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if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
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map->rec_frac[i][FEMALE]=rnum;
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}
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} else for (i=0; i<num_loci-1; i++) map->rec_frac[i][FEMALE]=0.0;
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- fgetln(fp);
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+ fgetln_(fp);
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for(i=0; i<num_loci-1; i++) {
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- if (nullstr(ln)) fgetln(fp);
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+ if (nullstr(ln)) fgetln_(fp);
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if (!itoken(&ln,iREQUIRED,&num)) send(CRASH);
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map->fix_interval[i]=num;
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}
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@@ -637,7 +637,7 @@
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matrix(map->error_lod,map->max_loci,raw.data.f2.num_indivs,real);
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}
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for (i=0; i<map->num_loci; i++) {
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- fgetln(fp);
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+ fgetln_(fp);
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if (!stoken(&ln,sREQUIRED,str) || !streq(str,"errors"))
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send(CRASH);
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if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
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@@ -646,9 +646,9 @@
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for(j=0; j<raw.data.f2.num_indivs; j++)
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map->error_lod[i][j]= 0.0;
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} else {
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- fgetln(fp);
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+ fgetln_(fp);
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for (j=0; j<raw.data.f2.num_indivs; j++) {
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- if (nullstr(ln)) fgetln(fp);
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+ if (nullstr(ln)) fgetln_(fp);
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if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
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map->error_lod[i][j]=rnum;
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}
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