mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2025-01-03 06:04:53 +00:00
Code Issues Releases Activity
e9d10f296e
freebsd-ports/biology/mapm3/files/patch-mapm-reader.c
Rong-En Fan 7e14529975 MAPMAKER/EXP is a linkage analysis package designed to help construct primary 
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>
2008-04-06 04:49:05 +00:00

192 lines
6.9 KiB
C
Raw Blame History

--- 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 @@
void getdataln(fp) /* get next nonblank,noncomment data file line */
FILE *fp;
-{ do { fgetln(fp); data_line++; } while (nullstr(ln)||ln[0]=='#'); }
+{ do { fgetln_(fp); data_line++; } while (nullstr(ln)||ln[0]=='#'); }
void baddata(reason) /* send data reading error message */
@@ -135,7 +135,7 @@
char tmpname[PATH_LENGTH+1];
make_filename(name,FORCE_EXTENSION,ext);
- strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,TEMP_EXT);
+ strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,WRS(TEMP_EXT));
fp=NULL; *exists=FALSE;
run {
@@ -162,7 +162,7 @@
bool exists;
{
char tmpname[PATH_LENGTH+1], oldname[PATH_LENGTH+1];
- strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,TEMP_EXT);
+ strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,WRS(TEMP_EXT));
strcpy(oldname,name); make_filename(oldname,FORCE_EXTENSION,oldext);
if (exists) { rename_file(name,oldname); }
@@ -214,7 +214,7 @@
raw.data.f2.cross_type);
print(" ok\n");
- make_filename(name,FORCE_EXTENSION,MAPS_EXT); strcpy(type,"map");
+ make_filename(name,FORCE_EXTENSION,WRS(MAPS_EXT)); strcpy(type,"map");
run {
fp2=NULL;
fp2=open_file(name,READ);
@@ -228,7 +228,7 @@
close_file(fp2);
} except_when(CANTOPEN) { } /* need a better handler */
- make_filename(name,FORCE_EXTENSION,TWO_EXT); strcpy(type,"two-point");
+ make_filename(name,FORCE_EXTENSION,WRS(TWO_EXT)); strcpy(type,"two-point");
run {
fp2=NULL;
fp2=open_file(name,READ);
@@ -240,7 +240,7 @@
close_file(fp2);
} except_when(CANTOPEN) { } /* need a better handler */
- make_filename(name,FORCE_EXTENSION,THREE_EXT); strcpy(type,"three-point");
+ make_filename(name,FORCE_EXTENSION,WRS(THREE_EXT)); strcpy(type,"three-point");
run {
fp2=NULL;
fp2=open_file(name,READ);
@@ -285,39 +285,39 @@
run {
strcpy(name,base_name);
if (save_genos_too) {
- fp= start_save_to_file(name,DATA_EXT,"genotype",&exists);
+ fp= start_save_to_file(name,WRS(DATA_EXT),"genotype",&exists);
write_f2_data(fp); /* deals with header and magic number */
close_file(fp); fp=NULL;
- finish_save_to_file(name,DATA_OLD,exists);
+ finish_save_to_file(name,WRS(DATA_OLD),exists);
}
- fp= start_save_to_file(name,MAPS_EXT,"map",&exists);
+ fp= start_save_to_file(name,WRS(MAPS_EXT),"map",&exists);
write_magic_number(fp,"map");
write_order_data(fp);
write_mapping_data(fp);
write_status(fp);
close_file(fp); fp=NULL;
- finish_save_to_file(name,MAPS_OLD,exists);
+ finish_save_to_file(name,WRS(MAPS_OLD),exists);
if (two_pt_touched) {
- fp= start_save_to_file(name,TWO_EXT,"two-point",&exists);
+ fp= start_save_to_file(name,WRS(TWO_EXT),"two-point",&exists);
write_magic_number(fp,"two-point");
write_two_pt(fp);
close_file(fp); fp=NULL;
- finish_save_to_file(name,TWO_OLD,exists);
+ finish_save_to_file(name,WRS(TWO_OLD),exists);
}
if (three_pt_touched) {
- fp= start_save_to_file(name,THREE_EXT,"three-point",&exists);
+ fp= start_save_to_file(name,WRS(THREE_EXT),"three-point",&exists);
write_magic_number(fp,"three-point");
write_three_pt(fp);
close_file(fp); fp=NULL;
- finish_save_to_file(name,THREE_OLD,exists);
+ finish_save_to_file(name,WRS(THREE_OLD),exists);
}
if (num_traits>0) {
- fp= start_save_to_file(name,TRAIT_EXT,"traits",&exists);
+ fp= start_save_to_file(name,WRS(TRAIT_EXT),"traits",&exists);
write_magic_number(fp,"trait");
write_traits(fp);
close_file(fp); fp=NULL;
- finish_save_to_file(name,TRAIT_OLD,exists);
+ finish_save_to_file(name,WRS(TRAIT_OLD),exists);
free_traits();
}
two_pt_touched= FALSE;
@@ -576,15 +576,15 @@
char header[MAXLINE+1];
if (raw.data.f2.cross_type==F2_INTERCROSS)
- fprint(fp,"prepared data f2 intercross\n");
+ fprint(fp,WRS("prepared data f2 intercross\n"));
else if (raw.data.f2.cross_type==F2_BACKCROSS)
- fprint(fp,"prepared data f2 backcross\n");
+ fprint(fp,WRS("prepared data f2 backcross\n"));
else if (raw.data.f2.cross_type==RI_SIB)
- fprint(fp,"prepared data f2 ri-sib\n");
+ fprint(fp,WRS("prepared data f2 ri-sib\n"));
else if (raw.data.f2.cross_type==RI_SELF)
- fprint(fp,"prepared data f2 ri-self\n");
+ fprint(fp,WRS("prepared data f2 ri-self\n"));
else if (raw.data.f2.cross_type==F3_SELF)
- fprint(fp,"prepared data f3\n");
+ fprint(fp,WRS("prepared data f3\n"));
sf(header,"%d %d %d\n",raw.filenumber,raw.data.f2.num_indivs,
raw.num_markers); fprint(fp,header);
@@ -593,7 +593,7 @@
sf(ps,"*%-10s ", raw.locus_name[i]);
fpr(fp);
for (j=0; j<raw.data.f2.num_indivs; j++) {
- if (j%50==0 && j!=0) fprint(fp,"\n ");
+ if (j%50==0 && j!=0) fprint(fp,WRS("\n "));
sf(ps,"%c",raw.data.f2.allele[i][j]);
fpr(fp);
}
@@ -828,9 +828,7 @@
char *symb;
{
/* CHANGED FOR THIS VERION - NOW READS "-AHBCD" */
-
- if (chr==symb[0]) return(MISSING_DATA);
- else if (chr==symb[1]) return(PARENTAL_TYPE_A);
+if (chr==symb[0]) return(MISSING_DATA); else if (chr==symb[1]) return(PARENTAL_TYPE_A);
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 @@
fnl(fp);
}
fnl(fp);
- fprint(fp,"#QTL only variables:\n");
- fprint(fp,"*Print mapm loci: 1\n");
- fprint(fp,"*Like tolerance: 0.001\n");
- fprint(fp,"*Brute force: 1\n");
- fprint(fp,"*Max intervals: -7\n");
- fprint(fp,"*Max continuous vars: -3\n");
- fprint(fp,"*Max wiggles: 0\n");
- fprint(fp,"*Max compares: 0\n");
- fprint(fp,"*Default units: 1\n");
- fprint(fp,"*Chromosomes: 0\n");
- fprint(fp,"*Number of contexts: 1\n");
- fprint(fp,"*Active context: 0\n");
+ fprint(fp,WRS("#QTL only variables:\n"));
+ fprint(fp,WRS("*Print mapm loci: 1\n"));
+ fprint(fp,WRS("*Like tolerance: 0.001\n"));
+ fprint(fp,WRS("*Brute force: 1\n"));
+ fprint(fp,WRS("*Max intervals: -7\n"));
+ fprint(fp,WRS("*Max continuous vars: -3\n"));
+ fprint(fp,WRS("*Max wiggles: 0\n"));
+ fprint(fp,WRS("*Max compares: 0\n"));
+ fprint(fp,WRS("*Default units: 1\n"));
+ fprint(fp,WRS("*Chromosomes: 0\n"));
+ fprint(fp,WRS("*Number of contexts: 1\n"));
+ fprint(fp,WRS("*Active context: 0\n"));
fnl(fp);
- fprint(fp,"*Context 1\n");
+ fprint(fp,WRS("*Context 1\n"));
if(num_traits == 1)
- fprint(fp,"*Trait: 0\n");
+ fprint(fp,WRS("*Trait: 0\n"));
else
- fprint(fp,"*Trait: -1\n");
- fprint(fp,"*Named sequences: 0\n");
- fprint(fp,"*Sequence history: 0\n");
+ fprint(fp,WRS("*Trait: -1\n"));
+ fprint(fp,WRS("*Named sequences: 0\n"));
+ fprint(fp,WRS("*Sequence history: 0\n"));
}
Reference in New Issue View Git Blame Copy Permalink