bool inclChrom(struct slName *chrom)
/* check if a chromosome should be included */
{
return !((noRandom && (endsWith(chrom->name, "_random")
|| startsWith("chrUn", chrom->name)))
|| (noHap && haplotype(chrom->name)));
}
bool inclChrom(char *name)
/* check if a chromosome should be included */
{
return !((noRandom && (endsWith(name, "_random")
|| startsWith("chrUn", name)
|| sameWord("chrNA", name) /* danRer */
|| sameWord("chrU", name))) /* dm */
|| (noHap && haplotype(name)));
}
static boolean inclChrom(char *chrom)
/* check if rows for chromosome should be included */
{
if (noRandom && (strstr(chrom, "_random") != NULL))
return FALSE;
if (noHap && haplotype(chrom))
return FALSE;
return TRUE;
}
void hap_transmit(int *n, int *ped, int *id, int *father, int *mother,
int *sex, int *aff, int *if_qt, double *qt,
int *m, int *markers,
int *multiple_cases, int *impute_using_affected,
char **ofname) {
Family *first, *f, *prev;
FILE *outfile;
int nn, mm, hr, iqt;
char *tmp;
nn = *n;
mm = *m;
iqt = *if_qt;
if (!*if_qt) qt = (double *) 0;
first = nuclear(nn, ped, id, father, mother, sex, aff, qt, mm, markers);
/* Multiple case treatment */
if (*multiple_cases) {
for (f=first; f; f=f->next) {
if (*multiple_cases == 1) {
prev = f;
f = expand_family(f, mm);
if (!f) goto overflow;
}
else if (*multiple_cases == 2) {
use_only_first(f);
}
}
}
/* Do remaining computations on families */
prev = (Family *) 0;
for (f=first; f; f=f->next) {
/* Impute missing parental genotypes */
impute_parent(f, mm, (int) *impute_using_affected);
/* Compute inheritance vectors */
inheritance(f, mm);
/* Resolve haplotype phase and transmission */
hr = haplotype(f, mm, 1);
/* If recombination, write error message */
if (hr<0) {
REprintf("*** Recombination/expaternity at locus %d *** ", -hr);
show_family(f);
}
/* If no information or recombination, omit family */
if (hr!=0) {
if (prev)
prev->next = f->next;
else
first = f->next;
}
else {
prev = f;
}
}
/* Write haplotypes to disk */
tmp = *ofname;
/* If no file name supplied, generate one */
if (!*tmp) {
tmp = tmpnam((char *) 0);
*ofname = tmp;
}
outfile = fopen(tmp, "wb");
if (outfile) {
*n = hap_write(first, mm, iqt, outfile);
fclose(outfile);
}
else {
REprintf("*** Couldn't open temporary file %s\n", tmp);
*n = 0;
}
/* Now return memory to system */
while (first) {
f = first;
first = first->next;
del_family(f);
}
return;
/* Memory overflow */
overflow:
warn("Memory overflow while or after expanding family", f);
}
int main(int argc, char** argv){
if(tomahawk::utility::IsBigEndian()){
std::cerr << tomahawk::utility::timestamp("ERROR") << "Tomahawk does not support big endian systems..." << std::endl;
return(1);
}
if(argc == 1){
tomahawk::ProgramMessage();
tomahawk::ProgramHelpDetailed();
return(1);
}
// Literal string input line
tomahawk::LITERAL_COMMAND_LINE = tomahawk::TOMAHAWK_PROGRAM_NAME;
for(int i = 1; i < argc; ++i)
tomahawk::LITERAL_COMMAND_LINE += " " + std::string(&argv[i][0]);
if(strcmp(&argv[1][0], "import") == 0){
return(import(argc, argv));
}
else if(strcmp(&argv[1][0], "calc") == 0){
return(calc(argc, argv));
} else if(strcmp(&argv[1][0], "calc-single") == 0 || strcmp(&argv[1][0], "scalc") == 0){
return(scalc(argc, argv));
}
else if(strcmp(&argv[1][0], "view") == 0){
return(view(argc, argv));
}
else if(strncmp(&argv[1][0], "sort", 4) == 0){
return(sort(argc, argv));
}
else if(strncmp(&argv[1][0], "concat", 6) == 0){
return(concat(argc, argv));
}
else if(strncmp(&argv[1][0], "stats", 5) == 0){
return(stats(argc, argv));
}
else if(strncmp(&argv[1][0], "aggregate", 8) == 0){
return(aggregate(argc, argv));
}
else if(strncmp(&argv[1][0], "haplotype", 9) == 0){
return(haplotype(argc, argv));
}
else if(strncmp(&argv[1][0], "relationship", 9) == 0){
return(relationship(argc, argv));
}
else if(strncmp(&argv[1][0], "decay", 5) == 0){
return(decay(argc, argv));
}
else if(strcmp(&argv[1][0], "--version") == 0 || strcmp(&argv[1][0], "version") == 0){
tomahawk::ProgramMessage(false);
return(0);
} else if(strcmp(&argv[1][0], "--help") == 0 || strcmp(&argv[1][0], "help") == 0){
tomahawk::ProgramMessage();
tomahawk::ProgramHelpDetailed();
return(0);
} else {
tomahawk::ProgramMessage();
tomahawk::ProgramHelpDetailed();
std::cerr << tomahawk::utility::timestamp("ERROR") << "Illegal command" << std::endl;
return(1);
}
return(1);
}
