/* @brief For bases, differentiate by (base, #occur); For deletions,
* differentiate by (D, #); for insertions, differentiate by
* (I, ins_str)
*
* @param [nuvars]: vars that were not previously called in [gvars]
*/
void pileup (var_t& nuvars, pileup_list_t& nulist, pileup_list_t& rmlist,
const pileup_list_t& pileuplist, const var_t& gvars,
const col_t& col, const std::vector<jeb_t>& jeb,
const GlobalParam& gParam, int iter) {
//{
// std::cout << "pos = " << col.ref_pos << "\n";
//}
int threshold = INT_MAX;
// ---------- generate profile and calculate lamda -------------
pileup_profile_t profile_info;
strset_t vars;
if (iter == 0) { // first iteration pop up the pic
pileup_profiling (profile_info, col, jeb, gParam);
if (profile_info.lamda_L) {
threshold = getThreshold (profile_info.lamda_L,
profile_info.p_L, gParam.bonferroni);
// ----------------- analyze profile and call vars ------------------
if (call_pileup_variant (vars, threshold, profile_info.LProfile)) {
nulist.L.insert(col.ref_pos);
}
}
if (profile_info.lamda_S) {
threshold = getThreshold (profile_info.lamda_S,
profile_info.p_S, gParam.bonferroni);
if (call_pileup_variant (vars, threshold, profile_info.SProfile)) {
nulist.S.insert(col.ref_pos);
}
}
add_var_entry (nuvars, col.ref_pos, vars);
{
// debug_print_var (nuvars);
}
} else { // not the first iteration
if (pileuplist.L.count(col.ref_pos) || pileuplist.S.count(col.ref_pos)) {
pileup_profiling (profile_info, col, jeb, gParam);
if (profile_info.lamda_L && pileuplist.L.count(col.ref_pos)) {
threshold = getThreshold (profile_info.lamda_L,
profile_info.p_L, gParam.bonferroni);
if (! call_pileup_variant (vars, threshold, profile_info.LProfile)){
rmlist.L.insert(col.ref_pos);
}
}
if (profile_info.lamda_S && pileuplist.S.count(col.ref_pos)) {
threshold = getThreshold (profile_info.lamda_S,
profile_info.p_S, gParam.bonferroni);
if (! call_pileup_variant (vars, threshold, profile_info.SProfile)) {
rmlist.S.insert(col.ref_pos);
}
}
// identify variants that were not yet in [gvars]
var_t::const_iterator it_gvar = gvars.find(col.ref_pos);
if (it_gvar != gvars.end()) {
strset_t diffs;
strset_t::const_iterator it_s = vars.begin();
for (; it_s != vars.end(); ++ it_s){
if (!it_gvar->second.count(*it_s)) diffs.insert(*it_s);
}
if (diffs.size()) add_var_entry(nuvars, col.ref_pos, diffs);
} else add_var_entry (nuvars, col.ref_pos, vars);
{
//debug_print_var (nuvars);
}
} // if
} // else
} // pileup
// adds an entry in the variable and handles arrays,
// if spec is a struct specifier definition,
// it will only check if struct is declared
// if spec is a struct specifier anonymous definition,
// anonymous_struct is used.
struct var_entry *
symtab_add_variable(struct tree_node * spec, struct tree_node * vardec) {
assert(spec -> unit_name == NODE_SPECIFIER);
assert(vardec -> unit_name == NODE_VARDEC);
// if variable with same name exists, just return NULL
// getting name requires a deep-in digging.
struct tree_node * identifier = vardec;
while (identifier -> flags == FLAG_VARDEC_ARRAY) identifier = identifier -> children[0];
identifier = identifier -> children[0];
assert(identifier -> unit_name == TOKEN_IDENTIFIER);
struct var_entry * e = add_var_entry(identifier -> id_extra -> name);
if (e == NULL) {
e = search_var_entry(identifier -> id_extra -> name);
if (e != NULL) {
semerrorpos(ERROR_VARIABLE_CONFLICT, vardec -> line);
printf("variable \'%s\' already declared at line %d\n",
e -> name, e -> defined_at);
} else {
struct struct_entry * se = search_struct_entry(identifier -> id_extra -> name);
semerrorpos(ERROR_OTHER, vardec -> line);
printf("variable \'%s\' name conflicts with struct declared at line %d\n",
se -> name, se -> defined_at);
}
return NULL;
}
// if spec is basic type, just next
if (spec -> flags == FLAG_SPECIFIER_BASIC) ;
// if spec is struct, check if that struct exists
struct struct_entry * strent = NULL;
if (spec -> flags == FLAG_SPECIFIER_STRUCT) {
const char *s_name;
if (spec -> children[0] -> flags == FLAG_STRUCTSPECIFIER_DEC) {
s_name = spec -> children[0] -> children[1] -> children[0] -> id_extra -> name;
strent = search_struct_entry(s_name);
if (strent == NULL) {
semerrorpos(ERROR_STRUCT_UNDEFINED, vardec -> line);
printf("struct \'%s\' not declared\n", s_name);
return NULL;
} else if (strent -> is_defined == 0) {
semerrorpos(ERROR_STRUCT_UNDEFINED, vardec -> line);
printf("struct \'%s\' is not defined\n", s_name);
return NULL;
}
} else if (spec -> children[0] -> flags == FLAG_STRUCTSPECIFIER_DEF) {
// a variable declared simultaneously with struct definition
if (spec -> children[0] -> children[1] -> flags == FLAG_OPTTAG_TAGGED) {
s_name = spec -> children[0] -> children[1] -> children[0] -> id_extra -> name;
strent = search_struct_entry(s_name);
if (strent == NULL) {
semerrorpos(ERROR_STRUCT_UNDEFINED, vardec -> line);
printf("struct \'%s\' is not defined\n", s_name);
return NULL;
}
} else if (spec -> children[0]-> children[1] -> flags == FLAG_OPTTAG_EMPTY) {
// an anonymous struct
strent = get_anonymous_struct();
if (strent == NULL) {
semerrorpos(ERROR_OTHER, vardec -> line);
printf("anonymous struct not set\n");
return NULL;
}
} else assert(0);
} else assert(0);
} // end if (spec -> flags == FLAG_SPECIFIER_STRUCT)
// now e points to a var_entry, filled with name
// spec points to a valid spec
e -> defined_at = identifier -> line;
if (vardec -> flags == FLAG_VARDEC_ARRAY) {
e -> type_flag = TYPE_ARRAY;
if (spec -> flags == FLAG_SPECIFIER_BASIC)
e -> t.array_type = construct_basic_array_type(spec, vardec);
else if (spec -> flags == FLAG_SPECIFIER_STRUCT)
e -> t.array_type = construct_struct_array_type(strent, vardec);
} else if (spec -> flags == FLAG_SPECIFIER_BASIC) {
e -> type_flag = TYPE_BASIC;
e -> t.basic_type = spec -> children[0] -> type_name;
} else {
assert(spec -> flags == FLAG_SPECIFIER_STRUCT);
e -> type_flag = TYPE_STRUCT;
e -> t.struct_type = strent;
}
return e;
} // end of function symtab_add_variable