struct variant *variantNew(char *chrom, unsigned start, unsigned end, unsigned numAlleles,
char *slashSepAlleles, char *refAllele, struct lm *lm)
/* Create a variant from basic information that is easy to extract from most other variant
* formats: coords, allele count, string of slash-separated alleles and reference allele. */
{
struct variant *variant;
// We have a new variant!
lmAllocVar(lm, variant);
variant->chrom = lmCloneString(lm, chrom);
variant->chromStart = start;
variant->chromEnd = end;
variant->numAlleles = numAlleles;
// get the alleles.
char *nextAlleleString = lmCloneString(lm, slashSepAlleles);
int alleleNumber = 0;
for( ; alleleNumber < numAlleles; alleleNumber++)
{
if (nextAlleleString == NULL)
errAbort("number of alleles in /-separated string doesn't match numAlleles");
char *thisAlleleString = nextAlleleString;
// advance pointer to next variant string
// probably there's some kent routine to do this behind the curtain
nextAlleleString = strchr(thisAlleleString, '/');
if (nextAlleleString) // null out '/' and move to next char
{
*nextAlleleString = 0;
nextAlleleString++;
}
boolean isRefAllele = (sameWord(thisAlleleString, refAllele) ||
(isEmpty(refAllele) && sameString(thisAlleleString, "-")));
int alleleStringLength = strlen(thisAlleleString);
if (isDash(thisAlleleString))
{
alleleStringLength = 0;
thisAlleleString[0] = '\0';
}
// we have a new allele!
struct allele *allele;
AllocVar(allele);
slAddHead(&variant->alleles, allele);
allele->variant = variant;
allele->length = alleleStringLength;
allele->sequence = lmCloneString(lm, thisAlleleString);
allele->isReference = isRefAllele;
}
slReverse(&variant->alleles);
return variant;
}
char* pathstr(char *arg, char character)
{
if(character != 'P' || character != 'C') //this is so we can use the one function for both PATH and CDPATH
{
printf("invalid argument '%c'\n", character);
exit(EXIT_FAILURE);
}
if (isDash(arg))
{
printf("argument has a '/' in it\n");
exit(EXIT_FAILURE);
}
char pathname[MAXPATHLEN];
switch(character)
{
case 'P':
sprintf(pathname, "%s", PATH);
break;
case 'C':
sprintf(pathname, "%s", CDPATH);
break;
}
int listlength = numElements(pathname);
char pathlist[listlength][MAXPATHLEN];
char *pathtemp = pathname; //this is so strtok doesn't modify our global variable
char *finalstr = malloc(MAXPATHLEN);
char *token;
char *ch = ":";
// get first token
token = strtok(pathtemp, ch);
int index = 0;
// walk through other tokens
while( token != NULL )
{
strcpy(pathlist[index], token);
++index;
token = strtok(NULL, ch);
} // now we should have an array of our directories
for(int i=0; i<listlength; i++)
{
char *dirname = pathlist[i];
DIR *dirp;
struct dirent *dp;
dirp = opendir(dirname);
if(dirp == NULL)
{
printf("directory doesn't exist"); //re word this
exit(EXIT_FAILURE);
}
while((dp = readdir(dirp)) != NULL)
{
if(strcmp(dp->d_name, arg))
{
sprintf(finalstr, "%s/%s", pathlist[i], arg);
}
}
closedir(dirp);
}
return finalstr;
}
