SEXP BWGFile_fromWIG(SEXP r_infile, SEXP r_seqlengths, SEXP r_outfile) {
pushRHandlers();
struct lm *lm = lmInit(0);
struct hash *lenHash = createIntHash(r_seqlengths);
struct bwgSection *sections =
bwgParseWig((char *)CHAR(asChar(r_infile)), FALSE, lenHash, itemsPerSlot,
lm);
bwgCreate(sections, lenHash, blockSize, itemsPerSlot, TRUE, TRUE, TRUE,
(char *)CHAR(asChar(r_outfile)));
lmCleanup(&lm);
freeHash(&lenHash);
popRHandlers();
return r_outfile;
}
/* --- .Call ENTRY POINT --- */
SEXP BWGSectionList_write(SEXP r_sections, SEXP r_seqlengths, SEXP r_compress,
SEXP r_file)
{
struct bwgSection *sections = NULL;
struct hash *lenHash = createIntHash(r_seqlengths);
if (r_sections != R_NilValue) {
sections = R_ExternalPtrAddr(r_sections);
slReverse(§ions);
}
pushRHandlers();
bwgCreate(sections, lenHash, blockSize, itemsPerSlot, asLogical(r_compress),
(char *)CHAR(asChar(r_file)));
freeHash(&lenHash);
popRHandlers();
return r_file;
}
pathExpr *createPathExpr(expr *f, locationPathExpr *l){
exception e;
pathExpr *pe = (pathExpr *)malloc(sizeof(pathExpr));
if (pe==NULL){
throwException2(out_of_mem,
"pathExpr allocation failed ");
return NULL;
}
Try{
pe->ih = createIntHash();
}
Catch(e){
free(pe);
Throw e;
}
pe->freeExpr = (free_Expr) &freePathExpr;
pe->evalBoolean = (eval_Boolean)&evalBoolean_pe;
pe->evalNodeSet = (eval_NodeSet)&evalNodeSet_pe;
pe->evalNumber = (eval_Number)&evalNumber_pe;
pe->evalString = (eval_String)&evalString_pe;
pe->isNumerical = (is_Numerical)&isNumerical_pe;
pe->isBoolean = (is_Boolean)&isBoolean_pe;
pe->isString = (is_String)&isString_pe;
pe->isNodeSet = (is_NodeSet)&isNodeSet_pe;
pe->requireContextSize = (require_ContextSize)&requireContextSize_pe;
pe->setContextSize = (set_ContextSize)&setContextSize_pe;
pe->setPosition = (set_Position)&setPosition_pe;
pe->reset = (reset_)&reset_pe;
pe->toString = (to_String)&toString_pe;
pe->adjust = (adjust_)&adjust_pe;
pe->fe = f;
pe->lpe= l;
pe->evalState = 0;
return pe;
}
